Methods for Treating and Detecting Johne's Disease in Cattle

Abstract

Biomarkers for identifying Johne's disease in cattle are presented herein, as are related methods, uses, agents, and kits comprising same. Methods for treating, detecting, quarantining, and diagnosing Johne's disease in cattle are presented herein.

Claims

1. A method for treating a bovine animal suspected of having Johne's disease, the method comprising treating the bovine animal identified as having Johne's disease with a therapeutically effective amount of at least one agent used to treat Johne's disease, wherein the bovine animal is identifiable as having Johne's disease by analyzing a biological sample isolated from the bovine animal for over-representation or under-representation of at least one polynucleotide relative to an internal standard region, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-16 or 134-164 and wherein the over-representation or under-representation of the at least one polynucleotide in the biological sample is a positive indicator of Johne's disease.

2. The method of claim 1, wherein the at least one polynucleotide comprising any one of SEQ ID NOs: 1-16 or 134-164 over-represented or under-represented relative to the internal standard region is at least two, at least three, at least four, or at least five of the polynucleotides comprising any one of SEQ ID NOs: 1-16 or 134-164.

3. The method of claim 1, wherein the biological sample is blood, a product derived from blood, or a fraction derived from blood.

4. The method of claim 3, wherein the product derived from blood is plasma or serum.

5. The method of claim 1, wherein detecting the over-representation or under-representation of the at least one polynucleotide relative to an internal standard region comprises at least one of a polymerase chain reaction (PCR)-based detection method, a hybridization-based method, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (MA), solid-phase enzyme immunoassay (EIA), mass spectrometry, and microarray analysis.

6. The method of claim 5, wherein the PCR-based detection method comprises amplifying nucleic acid sequences in the biological sample using primers that are specific for and capable of amplifying any one of SEQ ID NOs: 1-16 or 134-164, wherein the amplifying generates amplification products corresponding to any one of SEQ ID NOs: 1-16 or 134-164 when the biological sample comprises any one of SEQ ID NOs: 1-16 or 134-164.

7. The method of claim 5, wherein the PCR-based detection method is performed using at least one primer pair, wherein each primer pair of the at least one primer pair is specific for any one of SEQ ID NOs: 1-16 or 134-164.

8. The method of claim 7, wherein the primer pair specific for any one of SEQ ID NOs: 1-16 or 134-164 is any one of the primer pairs presented in Table 1.

9. The method of claim 6, further comprising sequencing the amplification products corresponding to any one of SEQ ID NOs: 1-16 or 134-164.

10. The method of claim 6, wherein the nucleic acid sequences comprise circulating nucleic acid.

11. The method of claim 1, wherein the at least one agent used to treat Johne's disease comprises at least one of antibiotic.

12. The method of claim 11, wherein the at least antibiotic is in a genus comprising rifabutin.

13. The method of claim 11, wherein the at least antibiotic is in a genus comprising clarithromycin.

14. The method of claim 11, wherein the at least antibiotic comprises rifabutin and clarithromycin.

15. The method of claim 1, wherein the bovine animal is monitored for Johne's disease.

16. A probe comprising a manmade nucleotide sequence capable of binding specifically to a polynucleotide comprising any one of SEQ ID NOs: 1-16 or 134-164 and at least one manmade tag conjugated thereto, wherein the manmade nucleotide sequence is complementary to the polynucleotide comprising any one of SEQ ID NOs: 1-16 or 134-164.

17. The probe of claim 16, wherein the manmade nucleotide sequence capable of binding specifically to a polynucleotide comprising any one of SEQ ID NOs: 1-16 or 134-164 exhibits at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, or at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% complementarity to any one of SEQ ID NOs: 1-16 or 134-164.

18. The probe of claim 16, wherein the manmade tag is a detectable marker.

19. An array comprising at least one probe comprising a manmade nucleotide sequence capable of binding specifically to a polynucleotide comprising any one of SEQ ID NOs: 1-16 or 134-164, wherein the manmade nucleotide sequence is complementary to the polynucleotide comprising any one of SEQ ID NOs: 1-16 or 134-164, wherein the at least one probe is bound to a solid surface.

20. The array of claim 19, comprising a microarray, gene chip, DNA chip, or a FILMARRAY.

Description

BRIEF DESCRIPTION OF THE FIGURES AND TABLES

[0051] The invention will now be described in relation to the tables.

[0052] Table 1 presents nucleic acid sequences for CNAs corresponding to either a CNA that is over-represented or under-represented in animals infected with MAP (SEQ ID NOs: 1-16 or 134-164) or an internal reference region that does not vary in MAP-infected or uninfected animals (SEQ ID NOs: 17-56.

[0053] FIG. 1 presents an exemplary Johne's disease algorithm workflow.

DETAILED DESCRIPTION OF THE INVENTION

[0054] Various embodiments will be described in detail with reference to the drawings and tables. Reference to various embodiments does not limit the scope of the claims attached hereto. Additionally, any examples set forth in this specification are not intended to be limiting and merely set forth some of the many possible embodiments.

[0055] JD/paratuberculosis is typically fatal disease of ruminants that can remain undetected for years in asymptomatic carriers, until they succumb to the disease and present clinically. Although largely asymptomatic, these carriers can spread JD among other herd members.

[0056] Accordingly, JD has serious economic consequences because a large percent of a given herd can become infected prior to any visible means of detecting the disease. MAP is present at high titers in the feces of infected animals and at lower titers in colostrum and milk. MAP is durable and largely resistant to environmental factors. MAP can survive on a pasture or in water for >1 year. Durability of MAP is likely due to its ability to form spores. The infection is typically acquired via the fecal-oral route, although it can be transmitted in utero and via nursing. Introduction of the disease into a non-infected herd is usually through herd expansion or replacement purchases. Infection is introduced via subclinically infected carriers. The long subclinical phase of MAP-induced disease makes it difficult to screen for the presence of infected animals.

[0057] Infection is typically acquired early in life, but clinical signs rarely develop in cattle before the age of two because progression to clinical disease is slow. MAP infection typically occurs in bovine animals within the first year of life, when animals are most susceptible to MAP infection, and likely occurs shortly after birth. Resistance to infection increases with age and cattle exposed as adults are much less likely to become infected. Infection occurs via ingestion of MAP when nursing on contaminated teats; consumption of milk, solid feed, or water contaminated by the organism; or licking and grooming behavior in a contaminated environment. After ingestion and uptake in the Peyer's patches of the lower small intestine, MAP infects macrophages in the gastrointestinal (GI) tract and associated lymph nodes. In that MAP is an intracellular pathogen, it proliferates inside infected macrophages, thereby creating reservoirs for ongoing infection. Infected macrophages eventually die and release high titer levels of MAP and/or are taken up by other phagocytic cells, thereby spreading MAP infection to other cells. MAP infection eventually provokes a chronic granulomatous enteritis that interferes with nutrient uptake and processing, leading to the cachexia typical of advanced infections. JD progression may take months to years to develop and is usually accompanied by a decline in cell-mediated immunity, a rise in serum antibody, and bacteremia once the infection is disseminated beyond the GI tract. Fecal shedding begins before clinical signs are apparent and animals in sub-clinical stages of infection are significant sources of transmission.

[0058] paratuberculosis in cattle (bovine animals) is characterized by weight loss and diarrhea in the late phases of infection, but infected animals can appear healthy for months to years. In cattle, diarrhea may be constant or intermittent; in sheep, goats, and other ruminants, diarrhea may not be seen. The diarrhea typically does not contain blood, mucus, or epithelial debris. As the diseases progresses, the diarrhea becomes more severe, further weight loss occurs, coat color may fade, and ventral and intermandibular edema may develop due to the loss of protein via enteropathy. In dairy cattle and goats, milk yield may drop or fail to reach expected levels. Animals are remain alert and are typically normal with respect to body temperature and appetite during phases of disease characterized by diarrhea. The disease is progressive and ultimately terminates in emaciation and death. In infected herds, the initial mortality rate may be low for a number of years, but as many as 50% of the animals may be infected subclinically in such herds and therefore, likely to succumb to disease eventually. The disease in sheep and goats is similar, but diarrhea is not a common feature. Advanced cases in sheep and goats typically shed wool easily.

[0059] Prior to the discoveries described herein, only two kinds of tests were used to diagnose JD. These tests rely on ELISA or PCR reagents and test kits to detect the presence of MAP in cattle by detecting MAP specific products. In most cases, these tests analyze feces or bodily fluids (such as milk) for the presence of MAP sequences or proteins. These tests are suboptimal, however, particularly with respect to the ability to detect MAP during early stages of infection and for animals not shedding bacteria into the environment. The lack of sensitivity of these conventional tests is evident when compared to the sensitivity of the methods described herein. The present inventors used the DNA sequence data set described herein to identify five animals as positive for MAP infection that the conventional prior art tests incorrectly identified as healthy animals. The lack of sensitivity and selectivity of the existing conventional Johne's testing assays is known in the industry, and may account, at least in part, for the low number of tests performed (approximately 25,000 per annum in Canada and Austria, respectively).

[0060] Further to the above, conventional Johne's testing assays are directed to detecting the presence of the infective agent (MAP). Accordingly, these technologies are limited to those stages of disease wherein larger quantities of MAP are shed by the animals. In contrast, methods described herein are based on measurements of the host response to the MAP challenge, which is less dependent on MAP levels in the animal. The present reagents and methods, therefore, exhibit higher selectivity and sensitivity than the conventional Johne's testing assays and, furthermore, facilitate diagnosis of JD at earlier, pre-clinical stages of MAP infection.

[0061] In general, the present disclosure describes polynucleotide sequences of circulating nucleic acids (CNA) isolated from blood serum of MAP-infected cattle. The polynucleotide sequences are over-represented or under-represented relative to an internal reference region in MAP-infected animals and can be used to detect MAP-infected animals before these animals display clinical symptoms of JD. Assays and methods comprising the polynucleotide sequences and/or primers and/or probes for amplifying or detecting the polynucleotide sequences in a sample (e.g., blood serum) isolated from cattle are also described and are useful for screening a broad range of cattle breeds for MAP infection.

[0062] Methods, reagents, and kits described herein relate to treating, quarantining, predicting and/or diagnosing JD in a bovine animal in advance of the appearance of symptoms of JD in the animal. In accordance with the experimental findings presented herein, methods, reagents, and kits described herein are useful for diagnosing JD in a bovine animal in advance of symptomatic presentation. Indeed, results presented herein demonstrate that methods, reagents, and kits described herein can diagnose JD in a bovine animal well in advance (e.g., years in advance) of clinical presentation. In light of results presented in the Examples, detection of over-representation or under-representation of at least one polynucleotide relative to an internal reference region in a body fluid sample (e.g., serum) isolated from a bovine animal, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-16 or 134-164, is a positive indicator that the bovine animal will develop JD symptoms. Accordingly, the methods, reagents, and kits described herein provide for diagnosis of JD at pre-clinical stages (asymptomatic stages) of the disease. Also encompassed herein are methods to assess over-representation or under-representation of at least one polynucleotide relative to an internal reference region, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-16 or 134-164, in body fluids and kits for such purposes.

[0063] In addition to plasma or serum, over-representation or under-representation of at least one polynucleotide (at least one of SEQ ID NOs: 1-16 or 134-164) relative to an internal reference region may be determined in other body fluids isolated from a bovine animal including: whole blood, a product derived from blood, or any fraction derived from blood (in addition to plasma or serum.

[0064] Any known method may be used for the determination of over-representation or under-representation of at least one polynucleotide (at least one of SEQ ID NOs: 1-16 or 134-164) relative to an internal reference region in body fluids. Methods encompassed for such determinations include: polymerase chain reaction (PCR) amplification with sequence specific primer pairs, a hybridization-based method, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), solid-phase enzyme immunoassay (EIA), mass spectrometry, microarray analysis, and any combination thereof. Such methods when used for determining risk for developing JD or predicting onset of JD are encompassed herein.

[0065] In a particular method for determining over-representation or under-representation of any one of SEQ ID NOs: 1-16 or 134-164 relative to an internal reference region in cattle body fluids, e.g. serum, the method calls for PCR amplification with sequence specific primer pairs. In an embodiment thereof, the PCR amplification is performed with at least one primer pair specific for any one of SEQ ID NOs: 1-16 or 134-164. Exemplary primer pairs for amplifying any one of SEQ ID NOs: 1-16 are presented in Table 1. Conditions for performing PCR amplifications are known in the art and presented in the Examples herein below. Such conditions may be determined based in part on the composition of a primer and/or primer pair and considerations relating to same are known in the art.

[0066] In another particular method for determining over-representation or under-representation of any one of SEQ ID NOs: 1-16 or 134-164 relative to an internal reference region in cattle body fluids, e.g. serum, the method calls for an ELISA. In one embodiment, the ELISA for at least one of SEQ ID NOs: 1-16 or 134-164 involves a sandwich array. In such an embodiment, PCR amplification of at least one of SEQ ID NOs: 1-16 or 134-164 may be performed as an initial step. Conventional microtiter plates may be coated with a first antibody, e.g. a guinea pig polyclonal antibody, directed against any one of SEQ ID NOs: 1-16 or 134-164. The plates are then blocked and the sample or standard is loaded. After incubation with, e.g., at least one of SEQ ID NOs: 1-16 or 134-164, a second antibody against any one of SEQ ID NOs: 1-16 or 134-164 is applied, e.g. a polyclonal rabbit antibody. A third antibody that detects the second antibody, e.g. an anti-rabbit antibody, conjugated to a suitable label, e.g. an enzyme for chromogenic detection, is then added. The plate is then developed with a substrate for the label in order to detect and quantify the label, which in turn serves as a measure of any one of SEQ ID NOs: 1-16 or 134-164 in the body fluid. This determination may then be compared to that of an internal reference region measured by similar methodology. If the label is an enzyme for chromogenic detection, the substrate is a color-generating substrate of the conjugated enzyme and the color reaction is subsequently detected in a microplate reader and compared to standards.

[0067] Suitable pairs of antibodies that may be used as first and second antibodies are any combination of, e.g., guinea pig, rat, mouse, rabbit, goat, chicken, donkey or horse antibodies. In a particular embodiment, the antibodies are polyclonal antibodies. In another particular embodiment, the antibodies are monoclonal antibodies or antibody fragments. Suitable labels include: chromogenic labels (enzymes that can be used to convert a substrate to a detectable colored or fluorescent compound), spectroscopic labels (e.g., fluorescent labels), and affinity labels which may be developed by an additional compound specific for the label, thereby facilitating detection and quantification, or any other label used in standard ELISA.

[0068] Other preferred methods for detection of any one of SEQ ID NOs: 1-16 or 134-164 include radioimmunoassay or competitive immunoassay using a single antibody and chemiluminescence detection on automated commercial analytical robots. Microparticle enhanced fluorescence, fluorescence polarized methodologies, or mass spectrometry may also be used. Detection devices, e.g. microarrays, are also useful components as readout systems for any one of SEQ ID NOs: 1-16 or 134-164.

[0069] Also encompassed herein are kits for assessing over-representation or under-representation of any one of SEQ ID NOs: 1-16 or 134-164 relative to an internal reference region for determining risk for developing JD, which kits may comprise apparatus and reagents for detecting at least one of SEQ ID NOs: 1-16 or 134-164. Apparatus and reagents considered for PCR amplification include: suitable PCR primer pairs specific for each of SEQ ID NOs: 1-16 or 134-164, amplification reagents, and thermocycling devices. With respect to ELISA, microtiter plates for ELISA, pre-coated ELISA plates, and plate covers are encompassed. Reagents useful for ELISA include those antibodies and solutions developed and designed for detecting each of SEQ ID NOs: 1-16 or 134-164. Standard solutions comprising each of SEQ ID NOs: 1-16 or 134-164 as positive controls may be included in such kits. Kits may further comprise hardware, such as pipettes, solutions such as buffers, blocking solutions and the like, filters, and directions for use thereof.

[0070] The following definitions are presented as an aid to understand the invention.

[0071] The term DNA means a polymer composed of deoxyriboucleotides.

[0072] The terms sample, biological sample, diagnostic sample, and the like refer to a material known or suspected of expressing or containing one or more polynucleotide or polypeptide markers. The diagnostic sample may be any tissue ((e.g., blood, and fractions thereof, including serum, etc.).

[0073] The terms polynucleotide and nucleic acid, used interchangeably herein, describe a polymer of any length, e.g., greater than about 10 bases, greater than about 100 bases, greater than about 500 bases, greater than 1000 bases, usually up to about 10,000 or more bases composed of nucleotides, such as deoxyribonucleotides or ribonucleotides, or compounds produced synthetically which can hybridize with naturally occurring nucleic acids in a sequence specific manner analogous to that of two naturally occurring nucleic acids in Watson-Crick base pairing interactions. Polynucleotide and nucleic acid include polynucleotides that encode a native-sequence polypeptide, a polypeptide variant, a portion of a polypeptide, a chimeric polypeptide, or an isoform, precursor, complex, modified form, or derivative of any of the foregoing, and any precursors thereof. Polynucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases, and/or their analogs, or any substrate that can be incorporated into a polymer by DNA or RNA polymerase or by a synthetic reaction. A polynucleotide may be modified after synthesis (e.g., by conjugation with a label, such as a radioactive, chemiluminescent, chemiflourescent, or fluorescent label, and the like). Other types of modifications to polynucleotides known to a person skilled in the art include substitution of one or more naturally-occurring nucleotides with an analog, internucleotide modifications (e.g., uncharged linkages, charged linkages), and the like.

[0074] Polynucleotides can also include circulating nucleic acids (CNA). The term circulating nucleic acid or CNA refers to free nucleic acid, including RNA and DNA, circulating in the blood. CNA can include gene transcripts or other polynucleotide sequences. CNA can be obtained from any applicable biological sample, including blood, plasma, serum, and the like.

[0075] Variants of the sequences described herein are sequences wherein at least one nucleotide differs from that of the native or wild-type sequence (or the complement thereof), by virtue of an insertion, deletion, modification and/or substitution of one or more nucleotides within the native sequence. Such variants generally have less than 100% sequence identity relative to a native sequence or its complement. Accordingly, a sequence variant may have a nucleotide sequence with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity relative to the native or wild-type sequence or complement thereof. Variants, furthermore, may include fragments of any length that retain a biological activity of the corresponding native sequence. Variants also include sequences wherein one or more nucleotides are added to the 5 or 3 end of, or within, a native sequence or its complement.

[0076] Percent sequence identity is defined herein as the percentage of nucleotides or in the candidate sequence that are identical to the nucleotides in the sequence of interest after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Methods and computer programs for the alignment of sequences are well known in the art, including, for example, BLAST algorithms.

[0077] Oligonucleotides include short, single-stranded polynucleotides that are at least seven nucleotides in length and less than about 250 nucleotides in length. The term polynucleotides includes oligonucleotides.

[0078] Label refers to a detectable compound or composition and labelling refers to the conjugation, fusion, or attachment of a detectable compound or composition to another. In some aspects described herein, the label is conjugated or fused directly or indirectly to a reagent, such as a polynucleotide probe or an antibody, and assists with the detection of the reagent to which it is conjugated or fused. The label itself can also be detectable (such as radioisotope labels or fluorescent labels and the like). In some aspects described herein, the label is an enzymatic label which catalyzes chemical alteration of a substrate compound or composition and results in a detectable product.

[0079] The term diagnosis, as used herein, refers to the identification or classification of a molecular or pathological state, disease, or condition (e.g., JD).). In a particular embodiment, JD is diagnosed in a subject (e.g., a bovine animal) in advance of onset of JD symptoms.

[0080] In a particular embodiment, a bovine subject is characterized as being at risk for developing JD because they have been exposed to or are suspected of having been exposed to MAP. Such exposures may be conveyed via exposure to a MAP-infected animal or an environmental feature (e.g., a field, water source, or food source) contaminated by bodily excretions/secretions (e.g., feces) of MAP-infected animals. Bovine subjects at risk for developing JD also include: very young cattle (e.g., less than one year old). Assays to evaluate risk for developing JD may also be implemented on all animals in a herd as a matter of routine practice. Such assays may also be performed in advance of acquisition of a new bovine animal so as to determine if the animal is a healthy, non-MAP-infected animal or an asymptomatic MAP-infected vector for JD transmission.

[0081] Primer refers to a polynucleotide capable of acting as a point of initiation of synthesis along a complementary strand when conditions are suitable for synthesis of a primer extension product. The synthesizing conditions include the presence of four different nucleotide bases (adenosine, cytidine, guanosine, thymidine/uridine) and at least one polymerization-inducing agent such as a reverse transcriptase or a DNA polymerase. The primers are present in a suitable buffer, which may include constituents which are co-factors or affect conditions such as pH and the like at various suitable temperatures. Primer includes single-stranded polynucleotide that is capable of hybridizing to nucleic acid and allowing the polymerization of a complementary nucleic acid, generally by providing a free 3-OH group. Double stranded sequences can also be utilized. Primers are typically at least about 15 nucleotides. In some embodiments, primers can have a length of from about 15 to about 30, about 15 to about 50, about 15 to about 75, about 15 to about 100, or about 15 to about 500 nucleotides.

[0082] Exemplary primer pairs specific for each of SEQ ID NOs: 1-56 are presented herein in Table 1. Such primer pairs are selected based on their specificity for a particular polynucleotide and may be optimized for use in connection with, e.g., PCR amplification. Polynucleotide-specific primer pairs may comprise primers that include variations within their sequence such that the primer is no longer 100% complementary to the polynucleotide for which it is specific. Primers comprising such variations are encompassed herein as long as the variations do not alter the ability of the primer to amplify the polynucleotide with specificity. Such variations may also include nucleotides and/or tags at the 5 and 3 ends of the primer that are not complementary the polynucleotide for which the primer is specific. It is also understood that a primer or primer pair may be complementary to sequences that flank any one of SEQ ID NOs: 1-56 and SEQ ID NOs: 134-164 in the bovine genome and thus, may be used to amplify one of SEQ ID NOs: 1-56 and SEQ ID NOs: 134-164 in keeping with methods described herein. Design of such primers and primer pairs is well within the capabilities of one of ordinary skill in the art having read the present specification.

[0083] A motif or sequence motif refers to a nucleotide sequence pattern that is generally conserved across multiple species. Polynucleotides can be derived from the motif. The polynucleotides can correspond to the entire sequence of the motif or a portion or portions of the motif.

[0084] Marker or biomarker refers to an indicator which can be detected in a sample, and includes predictive, diagnostic, and prognostic indicators and the like. The marker can be an indicator of a particular disease or disorder (e.g., JD) having certain molecular, pathological, histological, and/or clinical features. Exemplary biomarkers include, without limitation, polynucleotides, polypeptides, polypeptide and polynucleotide modifications (such as post-translational modifications and the like), carbohydrates, and/or glycolipid-based molecular markers. The presence, amount, or level of a marker associated with an increased clinical benefit to an individual is a detectable level of the marker in a sample. The presence, amount, or level of a marker can be measured by methods known to a person skilled in the art. The presence, amount, or level of a marker may be measured prior to treatment, during treatment, after treatment, or a combination of any of the foregoing.

[0085] Internal reference region refers to a nucleic acid fragment circulating in a bodily fluid (e.g., blood or a fraction thereof such as serum) that is present in the same amount in both control subjects (those subjects who are not infected by MAP, those subjects who do not have JD, and/or those subjects who are not at risk for developing JD) and subjects who are at risk for developing JD or who have JD, respectively, as determined by RT-PCR experiments. Internal reference regions provide a nucleic acid fragment which is represented in the bodily fluid at a particular level, against which representation of other nucleic acid sequences (e.g., any one of SEQ ID NOs: 1-16 or 134-164), which differ in control subjects and MAP-infected subjects and are therefore discriminatory, can be evaluated in a relative manner.

[0086] In one embodiment, over-representation refers to a fold increase (relative quantity RQ) relative to at least 2.sup.-delta-delta Cq of 2.

[0087] In one embodiment, under-representation refers to a fold decrease (relative quantity RQ) relative to minor as 2.sup.-delta-delta Cq of 0,5.

[0088] The Cq method normalizes disease-specific motifs within a sample by subtracting the Cq value of the internal reference region (reference motif) from the Cq value of the disease specific motifs.

[0089] The 2-Cq method calculates relative quantity (RQ) of normalized disease specific motifs between two sample types (i.e. healthy and diseased). Information from multiple reference motifs can be combined to improve accuracy.

[0090] As used herein, the term internal standard region may refer to a composite of at least two individual internal standard regions. Accordingly, internal standard region may refer to a composite of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, or 50 or more individual internal standard regions. Exemplary internal reference regions are presented in Table 1 (SEQ ID NOs: 17-56) and over-representation and under-representation may be determined relative to the level of at least one of the internal reference regions.

[0091] Further to the above, in an embodiment, detection of over-representation or under-representation of at least one polynucleotide relative to an internal reference region in a biological sample or body fluid sample (e.g., serum), wherein the at least one polynucleotide comprises any one of, e.g., SEQ ID NOs: 1-16, is considered as a positive indicator that a bovine subject from which the sample was isolated will develop JD. Over-representation may be used to refer to a fold increase (relative quantity RQ) calculated as 2-delta-delta Cq value of at least 2, whereas under-representation refers to a fold decrease (relative quantity RQ) calculated as 2-delta-delta Cq value of at most 0.5.

[0092] In another embodiment, for a given sample, the inventors use the Cq values for all (i.e. both old and new) regions (sequences) in the decision algorithm, which calculates the differences in Cq values (delta Cq) for certain informative pairs of regions and performs mathematical calculations on these delta Cq values. Based on these delta Cq values, the decision algorithm determines whether the collection of the delta Cq values as a whole is a positive indicator of Johne's disease. The informative pairs of regions to use, the specific decision algorithm to use, and the internal parameters of the decision algorithm are pre-determined based on a training dataset, but are fixed before the decision algorithm is used in a test setting. The decision algorithm is a binary (two-way, yes/no) classifier that assigns a class label (either diseased or healthy) to an input sample, thus determining the diagnosis. See FIG. 1 for flowchart illustrating the decision algorithm.

[0093] A specific set of decision algorithms (classifiers) are used with all sequences to determine the most informative region pairs and the final decision algorithm itself which together provide the classification performance on the training dataset. The current set of candidate classifiers comprises, without limitation, neural network, model averaged neural network, conditional inference random forest, distance weighted discrimination, and recursive partitioning. Sequences are then categorized as over-represented, under-represented, or internal reference based on the above classification scheme.

[0094] FIG. 1 presents an algorithm workflow illustrating a training phase and test phase of the algorithm whereby a determination of diseased versus healthy may be made in accordance with methods presented herein.

[0095] Encode refers to a polynucleotide encoding a polypeptide if, in its native state or when manipulated by methods well known to those skilled in the art, it can be transcribed and/or translated to produce the mRNA for the polypeptide and/or the polypeptide (or a fragment thereof). The anti-sense strand is the complement of such a nucleic acid, and the encoding sequence can be deduced therefrom.

[0096] Array or microarray refers to an ordered arrangement of hybridizable array elements on a substrate, such as solid substrate (e.g., glass slide and the like) or a semi-solid substrate (e.g., nitrocellulose membrane and the like). In some embodiments, the array elements may be polynucleotide probes (e.g. oligonucleotide). Array may include DNA microarrays (including cDNA microarrays, oligonucleotide microarrays, SNP microarrays, etc.), protein microarrays, peptide microarrays, antibody microarrays, and the like.

[0097] Amplification or amplifying refers to the production of one or more copies of a reference nucleic acid sequence or its complement. Amplification may be linear or exponential (e.g., in a polymerase chain reaction (PCR)). A nucleic acid copy produced from amplification may not have perfect sequence complementarity or identity relative to the reference sequence. In some embodiments, the copies can include nucleotide analogs, including deoxyinosine, intentional sequence alterations (such as alterations introduced through a primer that is hybridizable, but not fully complementary, to the template), and/or sequence errors that occur during the amplification process.

[0098] The terms expression and expression level, in general, are used interchangeably and generally refer to the amount of a marker in a sample. Expression generally refers to the process by which information (e.g., gene-encoded and/or epigenetic) is converted into the structures present and operating in the cell. Therefore, as used herein, expression can refer to transcription into a polynucleotide (such as mRNA and the like), translation into a polypeptide, or even polynucleotide and/or polypeptide modifications (e.g., post-translational modification of a polypeptide and the like). Fragments of the transcribed polynucleotide, the translated polypeptide, or polynucleotide and/or polypeptide modifications (such as post-translational modification of a polypeptide and the like) will also be regarded as expressed whether they originate from a transcript generated by alternative splicing or a degraded transcript, or from a post-translational processing of the polypeptide (e.g., by proteolysis). Expressed genes include those that are transcribed into a polynucleotide as mRNA and then translated into a polypeptide, and also those that are transcribed into RNA but not translated into a polypeptide (such as transfer and ribosomal RNAs and the like).

[0099] An isolated nucleic acid refers to a nucleic acid molecule that has been separated from a component of its natural environment. An isolated nucleic acid includes a nucleic acid molecule contained in cells that ordinarily contain the nucleic acid molecule. The nucleic acid molecule may be present extrachromosomally or at a chromosomal location that is different from its natural location.

[0100] An isolated antibody is an antibody which has been separated from a component of its natural environment. In some aspects described herein, an antibody is purified to greater than 95% or 99% purity as determined by methods known to a person skilled in the art, such as electrophoretic methods (e.g., SDS-PAGE, isoelectric focusing, capillary electrophoresis), chromatographic methods (e.g., ion exchange chromatography or reverse phase HPLC), and/or the like.

[0101] The term sequencing and its variants include obtaining sequence information from a strand of a nucleic acid molecule, typically by determining the identity of at least some nucleotides (including their nucleobase components) within the nucleic acid molecule. The term sequencing may also refer to determining the order of nucleotides (base sequences) in a nucleic acid sample (e.g. DNA or RNA). Many techniques are available and known to a person skilled in the art, such as Sanger sequencing, high-throughput sequencing technologies (such as the GS FLX platform offered by Roche Applied Science, Penzberg, Germany, based on pyro sequencing, or Illumina sequencing platforms, as offered by Illumina Inc., 5200 Illumina Way, San Diego, Calif. 92122, USA), and the like. High-throughput sequencing technologies refer to sequencing technologies having increased throughput as compared to traditional Sanger- and capillary-electrophoresis-based approaches (e.g., with the ability to generate hundreds of thousands or millions of relatively small sequence reads at a time). These high-through-put sequencing technologies include, but are not limited to, sequencing by synthesis, sequencing by ligation, pyrosequencing, sequencing by hybridization, and/or the like.

[0102] As used herein, reactive means the agent has affinity for, binds to, or is directed against specific CNAs. As further used herein, an agent includes a protein, polypeptide, peptide, nucleic acid (including DNA or RNA), antibody, Fab fragment, F(ab)2 fragment, molecule, compound, antibiotic, drug, and any combinations thereof. A Fab fragment is a univalent antigen-binding fragment of an antibody, which is produced by papain digestion. A F(ab)2 fragment is a divalent antigen-binding fragment of an antibody, which is produced by pepsin digestion. By way of example, the agent of the present invention can be labeled with a detectable marker. Agents that are reactive with CNAs can be identified by contacting the CNA with an agent of interest and assessing the ability of the agent to bind to the CNA.

[0103] In one embodiment of the present invention, the agent reactive with a JD biomarker is an antibody. Antibodies for use herein can be labeled with a detectable marker. Labeling of an antibody can be accomplished using one of a variety of labeling techniques, including peroxidase, chemiluminescent labels known in the art, and radioactive labels known in the art. The detectable marker of the present invention can be, for example, a nonradioactive or fluorescent marker, such as biotin, fluorescein (FITC), acridine, cholesterol, or carboxy-X-rhodamine (ROX), which can be detected using fluorescence and other imaging techniques readily known in the art. Alternatively, the detectable marker can be a radioactive marker, including, for example, a radioisotope. The radioisotope can be any isotope that emits detectable radiation, such as .sup.35S, .sup.32P, or .sup.3H. Radioactivity emitted by the radioisotope can be detected by techniques well known in the art. For example, gamma emission from the radioisotope can be detected using gamma imaging techniques, particularly scintigraphic imaging. By way of example, such an agent can be a high-affinity antibody labeled with a detectable marker.

[0104] Where the agent is an antibody reactive with a JD biomarker, a biological sample taken from a mammal (e.g., a bovine animal) can be purified by passage through an affinity column which contains the antibody having affinity to the JD biomarker as a ligand attached to a solid support, such as an insoluble organic polymer in the form of a bead, gel, or plate. The antibody attached to the solid support can be used in the form of a column. Examples of suitable solid supports include, without limitation, agarose, cellulose, dextran, polyacrylamide, polystyrene, sepharose, and other insoluble organic polymers. The antibody can be further attached to the solid support through a spacer molecule, if desired. Appropriate binding conditions (e.g., temperature, pH, and salt concentration) can be readily determined by the skilled artisan. By way of example, the antibody can be attached to a sepharose column, such as Sepharose 4B.

[0105] Alternatively, a diagnostic sample from a bovine animal can be assayed using hybridization analysis of nucleic acid extracted from the diagnostic sample taken from the cattle to determine the presence of a JD biomarker, such as a CNA. In this aspect of the invention, the hybridization analysis can be conducted using Northern blot analysis of mRNA. This method can also be conducted by performing a Southern blot analysis of DNA using at least one nucleic acid probe which hybridizes to CNAs (including amplified CNAs). The nucleic acid probes of the present invention can be prepared by a variety of techniques known to those skilled in the art, including, without limitation, the following: restriction enzyme digestion of nucleic acid; and automated synthesis of oligonucleotides having sequences which correspond to selected portions of the nucleotide sequence of the JD biomarker, using commercially-available oligonucleotide synthesizers.

[0106] The nucleic acid probes used herein can be DNA or RNA, and can vary in length from about 5-20 nucleotides or 10-20 nucleotides to the entire length of the nucleic acid encoding for a JD biomarker. In some embodiments, the nucleic acid probes are oligonucleotides. The nucleic acid used in the probes can be derived from mammalian polynucleotide sequence complementary to the JD biomarker. In addition, the nucleic acid probes of the present invention can be labeled with one or more detectable markers. Labeling of the nucleic acid probes can be accomplished using one of a number of methods known in the art (e.g., nick translation, end labeling, fill-in end labeling, polynucleotide kinase exchange reaction, random priming, SP6 polymerase (for riboprobe preparation)) along with one of a variety of labels (e.g., radioactive labels, such as .sup.35S, .sup.32P, or .sup.3H, or nonradioactive labels, such as biotin, fluorescein (FITC), acridine, cholesterol, or carboxy-X-rhodamine (ROX)). In some embodiments, these nucleic acid probes are used in an array or microarray.

[0107] In an exemplary approach, disease specific CNA motifs may be detected without any prior amplification step by implementing a hybridization-based procedure for the detection of JD-indicator markers using DNA probes labeled fluorescently. The probes may be the specific counterparts to the CNA molecules of interest and thus, hybridize to the JD-indicator CNA markers. Successful hybridization events produce a shift in the duration of the fluorescent signal, which shift can be measured and used as a parameter for the determination of the JD status of an animal.

[0108] In addition, the present invention provides a method of determining whether a bovine animal is at risk for JD, has been infected by MAP, and/or has already developed JD. The method includes analyzing a biological sample of the bovine animal for the presence of at least one JD biomarker, and optionally, further recommending a corroborative test for JD if the at least one JD biomarker is present in the biological sample. In some embodiments, the corroborative test includes ELISA, immunohistochemistry, and Western Blot/immunoblot or a combination of more than one of any of the foregoing.

[0109] In a further aspect, the present invention provides a method of determining progression of JD in cattle. The method includes analyzing a biological sample of the bovine animal for the presence of more than one JD biomarkers. The detection of the presence of more than one JD biomarker may be indicative of JD progressing in the bovine animal.

[0110] In the methods described herein, the step of analyzing a diagnostic sample can include obtaining the sample from the cattle (e.g., serum); using the serum directly or a diluted sample thereof (serum diluted in, e.g., water); amplifying the isolated nucleic acid using primers that are specific for or capable of amplifying a sequence corresponding to a JD CNA biomarker; and sequencing the amplified nucleic acid. In a more particular embodiment, the analyzing may include a step of isolating nucleic acids from the sample prior to amplification. n some embodiments, the isolated nucleic acid includes genomic DNA, mRNA, and/or cDNA obtained from mRNA. In some embodiments, the step of determining the representation of the at least one JD CNA marker includes use of at least one of a PCR-based detection method and a hybridization-based method. In some embodiments, the step of determining the representation of the at least one JD CNA marker includes an immunohistochemical analysis. In some embodiments, an array or a microarray is used for identifying the JD biomarker.

[0111] The diagnostic sample can be assayed for expression of JD biomarkers in vitro or in vivo. In addition, the diagnostic sample can be assayed for expression of JD biomarkers using all of the various assays and methods of detection and quantification described above.

[0112] The discovery that certain CNAs constitute JD biomarkers provides compositions and methods for identifying cattle at risk for developing JD and presents the potential for commercial application in the form of a test for the diagnosis of JD (including, e.g., early stage JD) and kits including same. The development of such a test or kit would provide general screening procedures; these procedures could assist in the early detection and diagnosis of JD in bovine subjects. Accordingly, the present invention further provides a kit for use as an assay of JD, comprising at least one agent reactive with a JD biomarker. The agent can be any of those described above, and can be used in any of the above-described assays or methods for detecting JD biomarkers.

[0113] Oligonucleotides complementary to a JD CNA biomarker can be designed based on the nucleotide sequence of the particular JD biomarker. A nucleotide sequence complementary to the selected partial sequence of the JD CNA biomarker can, e.g., be chemically synthesized using one of a variety of techniques known to those skilled in the art, including, without limitation, automated synthesis of oligonucleotides having sequences which correspond to a partial sequence of the JD CNA biomarker nucleotide sequence, or a variation sequence thereof, using commercially-available oligonucleotide synthesizers.

[0114] The present invention also provides the use of an oligonucleotide capable of identifying at least one JD CNA biomarker to determine the representation of same in a bovine subject. The oligonucleotide can be labelled with a detectable marker, such as a radioactive marker, fluorescent marker, the like, or a combination of any of the foregoing.

[0115] As described herein, the present inventors have identified DNA molecules, which circulate in the bovine bloodstream, the over- and under-representation of which can be used to discriminate between healthy and diseased animals afflicted by Johne's disease (i.e. bovine paratuberculosis) using DNA detection methods, including RT-PCR.

[0116] Serum from healthy individuals (controls) and diseased animals was harvested and initially stored at 80 degrees Celsius. Total DNA was extracted from the serum samples using the High Pure Viral Nucleic Acid Kit (Roche Applied Science; Cat. No. 11858874001). The DNA was amplified using the GenomePlex Single Cell Whole Genome Amplification Kit (Sigma; Cat. No. WGA4-500RXN) and purified using the GenElute PCR Clean-Up Kit (Sigma, Cat. No. NA1020-1KT). High-throughput paired-end DNA sequencing was performed by the University of Calgary's DNA Sequencing facility using Seq-It or NextSeq 500 sequencer machines. The resulting sequence reads were mapped to the bovine genome. Using an in-house Bioinformatics pipeline, which was established on the high-performance Bioinformatics infrastructure at the Institute of Computational Biotechnology, the present inventors have identified DNA motifs, that are present at distinctively high or distinctively low read count numbers in diseased animals, when compared to controls, corresponding to motifs that are over-represented and under-represented in JD, respectively. The motifs identified are the result of the host response (i.e. the response of the animal's body) to the infection with Mycobacterium avium ssp. paratuberculosis. The DNA motifs thus identified were used as targets for the development of a real-time Polymerase-Chain Reaction (RT-PCR) assay. In addition to the motifs that are present at distinctively different levels in healthy and infected animals (markers: over- and under-represented CNAs), motifs that are present at highly similar levels in healthy and diseased animals (internal reference regions) were also identified. The identification of internal reference regions facilitates normalization and accurate evaluation of the detected quantities of over- and under-represented JD-indicative DNA motifs across different animal samples and RT-PCR reactions. The RT-PCR-evaluated motifs, which are used to discriminate between healthy and diseased animals in a statistically significant manner, may be assessed as individual markers of JD or in combination with other motifs as a group.

[0117] Another aspect of the invention is arrays comprising one of more polynucleotides of the disclosure, PCR primers and/or probes for amplifying and/or detecting polynucleotides of the inventions, and methods of detecting JD indicative CNAs comprising an array or PCR primers and/or probes according to the disclosure.

[0118] Arrays comprising one of more polynucleotides of the disclosure, PCR primers and/or probes for amplifying and/or detecting polynucleotides (CNAs) described herein, and methods for detecting risk for developing JD comprising an array or PCR primers and/or probes are encompassed herein.

[0119] One of more polynucleotide sequences of the disclosure can be incorporated onto a sequence array, such as a biochip, DNA chip, BiofireDX filmarray and other filmarrays, microarray, macroarray, and the like, for screening, e.g., serum separated from whole blood from bovine animals for JD risk. Alternatively, CNAs can be extracted from the sample for screening on the array. Arrays are generally solid supports upon which a collection of polynucleotides and/or primers and/or probes are placed at defined locations on the array, either by spotting, printing, or direct synthesis. The array can include probes corresponding to one or more of the polynucleotides described herein (e.g., at least one of SEQ ID NOs: 1-56 and SEQ ID NOs: 134-164 and/or primers and/or probes for amplifying and/or detecting one or more polynucleotides of SEQ ID NOs: 1-56 and SEQ ID NOs: 134-164).

[0120] The underlying principle of arrays is base pairing or hybridization i.e., A-T and G-C for DNA, and A-U and G-C for RNA. A sample from a mammal (e.g., a bovine animal) is allowed to hybridize with the polynucleotides and/or primers and/or probes on the array providing an expression profile/pattern of CNA. The CNA expression pattern of JD-indicator sequences can be used to determine if a bovine animal is at risk for developing JD. The array can be prepared by any method known in the art. In some embodiments, a microarray is prepared generally as disclosed in U.S. Pat. No. 7,655,397, the entirety of which is hereby incorporated by reference.

[0121] In some embodiments, the array comprises at least 4 polynucleotides selected from polynucleotides comprising or consisting of SEQ ID NOs: 1-16 or 134-164 or primers or probes specific for at least 4 of SEQ ID NOs: 1-16 or 134-164. In another embodiment, the array comprises at least 8 polynucleotides selected from the polynucleotides comprising or consisting of SEQ ID NOs: 1-16 or 134-164 or primers or probes specific for at least 8 of SEQ ID NOs: 1-16 or 134-164. In some embodiments, the array comprises up to 19 polynucleotides comprising or consisting of SEQ ID NOs: 1-16 or 134-164 or primers or probes specific for at least 19 of SEQ ID NOs: 1-16 or 134-164. Arrays described herein may further comprise at least one of SEQ ID NOs: 17-56, which are internal reference region sequences. The array generally includes many copies of the selected polynucleotides to facilitate detection. In some embodiments, the array comprises a million or more copies of each of the selected polynucleotides.

[0122] Probes for detecting polynucleotides described herein can be designed and prepared using conventional methods. Software for modeling and designing probes and primers, including determining hybridization and annealing conditions, for detecting a specific polynucleotide sequence are publicly available, and include for example those of Integrated DNA Technologies, LightCycler Probe Design Software (Roche Applied Science), Primer3 (Simgene), and FastPCR (PrimerDigital). See also techniques described by Illumina (Illumina Inc., 5200 Illumina Way, San Diego, Calif. 92122, USA).

[0123] The array can include positive indicator for JD sequences and/or probes for detecting same and negative and/or positive control sequences and/or probes.

[0124] Polynucleotides described herein can be amplified and/or detected via PCR, including but not limited to real-time PCR, multiplex PCR, nested PCR, solid phase PCR, miniprimer PCR, and the like. Primers and probes for amplifying and/or detecting polynucleotides described herein can be designed and prepared using conventional methods. Software for modeling and designing primers and probes, including determining hybridization, melting, annealing, and/or extensions conditions, for amplifying and/or detecting a specific polynucleotide sequence are publicly available, and include for example LightCycler Probe Design Software (Roche Applied Science), Primer3 (Simgene), and FastPCR (PrimerDigital). See also techniques described by Illumina (Illumina Inc., 5200 Illumina Way, San Diego, Calif. 92122, USA). PCR conditions generally include the presence of four different nucleotide bases (adenosine, cytidine, guanosine, thymidine/uridine) and at least one polymerization-inducing agent such as a reverse transcriptase or a DNA polymerase. The primers are generally present in a suitable buffer, which may include constituents, which are co-factors or affect conditions such as pH and the like at various suitable temperatures. The primers are preferably single-strand nucleotide sequences, such that amplification efficiency of the desired polynucleotide is optimized. Double-stranded nucleotide sequences can also be utilized. The primers are typically at least about 15 nucleotides. In some embodiments, the primers can have a length of from about 15 to about 30, about 15 to about 50, about 15 to about 75, about 15 to about 100, or about 15 to about 500 nucleotides.

[0125] In some embodiments, primer sets are designed to amplify one or more of the at risk for JD-indicative polynucleotides comprising or consisting of SEQ ID NOs: 1-16 or 134-164 and then the PCR products of the primer sets are screened for JD-indicator sequences on an array as described herein. Primer sets designed to amplify one or more of the at least one of SEQ ID NOs: 17-56, which are internal reference region sequences, are also encompassed.

[0126] Diagnostic kits comprising one or more primer pairs, and optional probes, for amplifying and detecting one or more polynucleotides described herein are also provided. The kit can optionally include nucleotide bases (adenosine, cytidine, guanosine, thymidine/uridine) and at least one polymerization-inducing agent such as a reverse transcriptase or a DNA polymerase. The kit can optionally include a suitable primer buffer, which may include constituents which are co-factors or affect conditions such as pH and the like at various suitable temperatures. The kit can optionally include an array as described herein.

[0127] The primers provided in the diagnostic kit are generally provided at least in pairs (forward primer and reverse primer) for amplifying a specific polynucleotide sequence. These primers can be used to amplify and detect CNAs in blood serum from cattle, or any other appropriate biological sample from cattle that may contain CNAs. Alternatively, CNAs can be extracted from the sample and then amplified by PCR using a diagnostic kit of the disclosure. The CNA expression pattern of JD-indicative sequences detected by the diagnostic kit can be used to determine if a bovine animal is at risk for developing JD even at a stage wherein no clinical symptoms of JD are apparent.

[0128] In some embodiments, the kit comprises primers for amplifying at least 4 polynucleotides selected from the polynucleotides comprising or consisting of SEQ ID NOs: 1-16 or 134-164, and optionally one or more probes for detecting the amplified product. In another embodiment, the kit comprises primers for amplifying at least 8 polynucleotides selected from the polynucleotides comprising or consisting of SEQ ID NOs: 1-16 or 134-164, and optionally one or more probes for detecting the amplified product. In some embodiments, the kit comprises primers for amplifying up to 16 polynucleotides comprising or consisting of SEQ ID NOs: 1-16 or 134-164, and optionally one or more probes for detecting the amplified product.

Treatment of MAP-Infected Cattle

[0129] In that JD is caused by MAP, antimicrobial therapy is envisioned as a reasonable therapeutic regimen for treatment thereof. In a particular embodiment, the antimicrobial therapy comprises administration of antibiotics, which may be administered alone or in conjunction with anti-inflammatory therapy. The choice of antibiotic used for treating a bovine animal afflicted with JD is based on the drug susceptibility profiles of MAP clinical isolates. Macrolide drugs, such as, for example, clarithromycin and azithromycin exhibit the greatest in vitro efficacy. The rifampicin family of antibiotics also exhibits in vitro efficacy against MAP. Accordingly, in a particular embodiment, at least one of a macrolide drug (such as, e.g., clarithromycin, azithromycin, amikacin, ciprofloxacin, and levofloxacin) and an antibiotic in the rifampicin family (e.g., rifampicin, rifabutin, and ethambutol) is administered to a bovine animal afflicted with JD. An exemplary anti-inflammatory therapy that may be administered in conjunction with antibiotic therapy involves administration of non-steroidal anti-inflammatory agents to the bovine animal afflicted with JD.

[0130] In a particular embodiment, a bovine animal which is identified as MAP-infected using methods and/or reagents described herein is treated with 20 mg/kg of an antibiotic in the rifampicin family (e.g., rifampicin, rifabutin, and ethambutol) alone or in combination with 20 mg/kg of isoniazid. In a more particular embodiment, a bovine animal which is identified as MAP-infected using methods and/or reagents described herein is treated with 10-20 mg/kg of rifampicin alone or in combination with 20 mg/kg of isoniazid. In a still more particular embodiment, a bovine animal which is identified as MAP-infected using methods and/or reagents described herein is treated with 10-20 mg/kg of rifampin.

[0131] The ionophore antibiotic, monensin, also offers promise as a therapeutic agent for treating JD in adult cattle and calves. Monensin may also serve as a chemoprophylactic for calves. Monensin inhibits in vitro growth of certain MAP strains. Data from in vivo studies is, moreover, encouraging. Provision of monensin to adult cattle naturally infected with MAP has been associated with modest improvements in histopathology scores (i.e., less tissue damage resulting from infection), decline in fecal shedding rate, and/or reduced odds of testing positive on a milk ELISA. Monensin used as a chemoprophylactic in calf milk replacer in dairy calves resulted in reduced tissue colonization and MAP fecal shedding.

[0132] Accordingly, monensin may be administered to a bovine animal which is identified as MAP-infected using methods and/or reagents described herein to reduce MAP infection levels. In a more particular embodiment, a bovine animal which is identified as MAP-infected using methods and/or reagents described herein is treated with Monensin CRC (Rumensin CRC) administered in capsule form supplied by Elanco, a Division Eli Lilly Canada, Guelph, Ont., Canada. The monensin CRC is a sustained-release intraruminal device that has a medicated core containing 32 g monensin in a hexaglycerol distearate matrix (45% monensin). Each capsule delivers its product over an average period of 95 days (Rumensin CRC, Veterinary Reference Guide, Elanco Animal Health, A Division of Eli Lilly Canada Inc.). Capsules are administered orally with a specially designed administration tool. In another embodiment, monensin may be administered to a bovine animal which is identified as MAP-infected using methods and/or reagents described herein at a dose of 450 mg/head for 120 days.

[0133] In another embodiment, a bovine animal which is identified as MAP-infected using methods and/or reagents described herein is treated daily with 10-20 mg/kg isoniazid.

[0134] In another embodiment, a bovine animal which is identified as MAP-infected using methods and/or reagents described herein is treated daily with 2 mg/kg to 15 mg/kg of clofazimine administered orally. In yet another embodiment, a bovine animal which is identified as MAP-infected using methods and/or reagents described herein is treated daily with 600-1,000 mg of clofazimine administered orally.

[0135] In a further embodiment, a bovine animal which is identified as MAP-infected using methods and/or reagents described herein is treated daily with 10-20 mg/kg of rifampin administered orally.

[0136] In another embodiment, a bovine animal which is identified as MAP-infected using methods and/or reagents described herein is treated daily with 20 mg/kg of gallium nitrate.

[0137] In yet another embodiment, a bovine animal which is identified as MAP-infected using methods and/or reagents described herein is administered a once-daily oral treatment comprising rifampin (10-20 mg/kg) and isoniazid (10-20 mg/kg). In a more particular embodiment, monensin should be administered in conjunction with rifampin (10-20 mg/kg) and isoniazid (10-20 mg/kg) at a dose of 200 mg/head/day monensin for beef cattle or a dose of 410 mg/head/day monensin for dairy cattle

[0138] The aforementioned therapeutic regimens may be supplemented with levamisole as an adjunctive therapy. In a particular embodiment thereof, the levamisole is administered via weekly injections at a dosage of 2.5 mg/kg.

[0139] The present invention is described in the following Examples, which are set forth to aid in an understanding of the invention, and should not be construed to limit in any way the scope of the invention as defined in the claims which follow thereafter.

EXAMPLES

Example 1Identification of Unique Johne's Disease-Associated Motifs in CNAS

[0140] The present inventors have identified CNAs, the over- and under-representation of which can be used to discriminate between healthy cattle and diseased cattle afflicted by Johne's disease (i.e. bovine paratuberculosis) using DNA detection methods, including RT-PCR.

[0141] Serum from healthy individuals (controls) and diseased animals was harvested and total DNA was extracted from the serum samples. The DNA was amplified and high-throughput paired-end DNA sequencing was performed. The resulting sequence reads were mapped to the bovine genome. The present inventors identified DNA motifs, which were present at different read count numbers in MAP-infected animals when compared to controls. The motifs identified reflect the host response to the infection with Mycobacterium avium ssp. paratuberculosis. The DNA motifs identified were used as targets for the development of a RT-PCR assay. In addition to the motifs, which are present at different levels in healthy and infected animals (markers; over- and under-represented CNAs), motifs which were present at the same level in healthy and infected animals (internal reference regions) were also identified. The identification of internal reference regions facilitates normalization of the results. The RT-PCR-evaluated motifs, which are used to discriminate between healthy and infected animals in a statistically significant manner, may be assessed as individual markers of JD or in combination with each other.

[0142] 1 bov-jd-0001: 25:32377622-32377759; Over-Represented

[0143] 1.1 Sequence

TABLE-US-00001 (SEQ ID NO: 1) TACCATGGTGACCACGGGTGACGGGGAATCAGGGTTCGATTCCGGAGAGG GAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAAT TACCCACTCCCGACCCGGGGAGGTAGTGACGAAAAATA

[0144] 1.2 Sequence with 25 bp Surroundings

TABLE-US-00002 (SEQ ID NO: 2) AACTTTCGATGGTAGTCGCTGTGCCTACCATGGTGACCACGGGTGACGGG GAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATC CAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGACCCGGGGAGGTA GTGACGAAAAATAACAATACAGGACTCTTTGAGGCC

[0145] 1.3 Annotation

[0146] 1.3.1 Genes

[0147] 1.3.2 Next Upstream Gene

RefSeqID: NM_001192067

[0148] Gene name: GALNT17
Product: putative polypeptide N-acetylgalactosaminyltransferase-like protein 3
Translation start: 29391799

Translation end: 29824281 Distance to

[0149] region end: 2553340 Exons: 11

[0150] 1.3.3 Next Downstream Gene

RefSeqID: NR_046257

[0151] Gene name: RN45S Product:
Translation start: 32380939

Translation end: 32469510 Distance to

[0152] region end: 3181 Exons: 9

[0153] 1.3.4 Repeats

Repeat name: SSU-rRNA_Hsa Repeat
class: rRNA
Repeat family: rRNA Repeat start:
32377234

Repeat end: 32377936

[0154] 2 bov-jd-0002: 18:58238154-58238329; Over-Represented

[0155] 2.1 Sequence

TABLE-US-00003 (SEQ ID NO: 3) GCTATCCTGAGGGAAACTTCGGAGGGAACCAGCTACTAGATGGTTCGATT AGTCTTTCGCCCCTATACCCAGGTCGGACGACCGATTTGCACGTCAGGAC CGCTACGGACCTCCACCAGAGTTTCCTCTGGCTTCGCCCTGCCCAGGCAT AGTTCACCATCTTTCGGGTCCTAACA

[0156] 2.2 Sequence with 25 bp Surroundings

TABLE-US-00004 (SEQ ID NO: 4) GGTCTGTGCGTTTGCGAGAGCGCCAGCTATCCTGAGGGAAACTTCGGAGG GAACCAGCTACTAGATGGTTCGATTAGTCTTTCGCCCCTATACCCAGGTC GGACGACCGATTTGCACGTCAGGACCGCTACGGACCTCCACCAGAGTTTC CTCTGGCTTCGCCCTGCCCAGGCATAGTTCACCATCTTTCGGGTCCTAAC ACGTGCGCTCATGCTCCACCTCCCC

[0157] 2.3 Annotation

[0158] 2.3.1 Genes

[0159] 2.3.2 Next Upstream Gene

RefSeqID: NM_001075708

[0160] Gene name: ZNF350
Product: zinc finger protein 350
Translation start: 58212121

Translation end: 58220105 Distance to

[0161] region end: 18048 Exons: 5

[0162] 2.3.3 Next Downstream Gene

RefSeqID: NM_001037477

[0163] Gene name: PPP2R1A
Product: serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
Translation start: 58425841

Translation end: 58448792 Distance to

[0164] region end: 187513 Exons: 15

[0165] 2.3.4 Repeats

Repeat name: LSU-rRNA_Hsa Repeat
class: rRNA
Repeat family: rRNA Repeat start:
58238080

Repeat end: 58238908

[0166] 3 bov-jd-0003: X:62078561-62078748; Over-Represented

[0167] 3.1 Sequence

TABLE-US-00005 (SEQ ID NO: 5) TTCGCTGGATAGTAGGTAGGGACAGTGGGAATCTCGTTCATCCATTCATG CGCGTCACTAATTAGATGACGAGGCATTTGGCTACCTTAAGAGAGTCATA GTTACTCCCGCCGTTTACCCGCGCTTCATTGAATTTCTTCACTTTGACAT TCAGAGCACTGGGCAGAAATCACATCGCGTCAACACCC

[0168] 3.2 Sequence with 25 bp Surroundings

TABLE-US-00006 (SEQ ID NO: 6) CCAAGCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGTAGGTAGGGACAG TGGGAATCTCGTTCATCCATTCATGCGCGTCACTAATTAGATGACGAGGC ATTTGGCTACCTTAAGAGAGTCATAGTTACTCCCGCCGTTTACCCGCGCT TCATTGAATTTCTTCACTTTGACATTCAGAGCACTGGGCAGAAATCACAT CGCGTCAACACCCGCCGCGGGCCTTCGCGATGCTTTG

[0169] 3.3 Annotation

[0170] 3.3.1 Genes

[0171] 3.3.2 Next Upstream Gene

RefSeqID: NM_001001171

[0172] Gene name: ATG4A
Product: cysteine protease ATG4A Translation
start: 61017761

Translation end: 61050945 Distance to

[0173] region end: 1027615 Exons: 12

[0174] 3.3.3 Next Downstream Gene

RefSeqID: NM_174549

[0175] Gene name: GUCY2F
Product: retinal guanylyl cyclase 2 precursor
Translation start: 62214455

Translation end: 62364957 Distance to

[0176] region end: 135708 Exons: 20

[0177] 3.3.4 Repeats

Repeat name: LSU-rRNA_Hsa Repeat
class: rRNA
Repeat family: rRNA
Repeat start: 62078135

Repeat end: 62078930

[0178] 4 bov-jd-0004: 21:2014523-2014688; Over-Represented

[0179] 4.1 Sequence

TABLE-US-00007 (SEQ ID NO: 7) AGATGGATTTAGAGTGTGTGGCTGTTGTGTGTGGTTCAGAATTCTGAGTA GTCCTTTCAGGGATCACCCAAAAGCTCAGACAAAGCGTGAGCCCTTCACG TGGACTGTGCTGTGCGTCAGAAAGATAATACGAGCCACCTACACAATCTA AAATTTCCTAAAAACC

[0180] 4.2 Sequence with 25 bp Surroundings

TABLE-US-00008 (SEQ ID NO: 8) TGAACACTGAATGTGTTTGCATTATAGATGGATTTAGAGTGTGTGGCTGT TGTGTGTGGTTCAGAATTCTGAGTAGTCCTTTCAGGGATCACCCAAAAGC TCAGACAAAGCGTGAGCCCTTCACGTGGACTGTGCTGTGCGTCAGAAAGA TAATACGAGCCACCTACACAATCTAAAATTTCCTAAAAACCAACGGGCTA CTCGACGTCCTCCTT

[0181] 4.3 Annotation

[0182] 4.3.1 Genes

[0183] 4.3.2 Next Upstream Gene

RefSeqID: NM_001014982

[0184] Gene name: NDN Product:
necdin Translation start: 736182

Translation end: 737792 Distance to

[0185] region end: 1276730 Exons: 1

[0186] 4.3.3 Next Downstream Gene

RefSeqID: NM_001098462

[0187] Gene name: UBE3A
Product: ubiquitin-protein ligase E3A Translation
start: 2346808

Translation end: 2410193 Distance to

[0188] region end: 332121 Exons: 12

[0189] 4.3.4 Repeats

Repeat name: MER33 Repeat
class: DNA
Repeat family: hAT-Charlie Repeat start:
2014704

Repeat end: 2014825

[0190] 5 bov-jd-0005: 1:33090510-33090673; Over-Represented

[0191] 5.1 Sequence

TABLE-US-00009 (SEQ ID NO: 9) AGCTGAAGTGGTGGGATAGTGTAGTTTGTGTGTCATAGGAATCTCCTCAA AGGATGATGTCATCAGTGTGAGGTCCTAATTGTGTCCTAGAAAAAGTTAG AGCTGGTGAAAATGTTGCCTTCAAAGACTGTGTGAGATGGCAGGTGTGGA CACTGGCCCCACTG

[0192] 5.2 Sequence with 25 bp Surroundings

TABLE-US-00010 (SEQ ID NO: 10) TTTACCAAAAAGTTTTCAGGAGCTTAGCTGAAGTGGTGGGATAGTGTAGT TTGTGTGTCATAGGAATCTCCTCAAAGGATGATGTCATCAGTGTGAGGTC CTAATTGTGTCCTAGAAAAAGTTAGAGCTGGTGAAAATGTTGCCTTCAAA GACTGTGTGAGATGGCAGGTGTGGACACTGGCCCCACTGAGTAGACAGGT GACGGTGTATCGT

[0193] 5.3 Annotation

[0194] 5.3.1 Genes

[0195] 5.3.2 Next Upstream Gene

RefSeqID: NM_001122729

[0196] Gene name: GBE1
Product: 1,4-alpha-glucan-branching enzyme
Translation start: 28659455

Translation end: 28972472 Distance to

[0197] region end: 4118037 Exons: 15

[0198] 5.3.3 Next Downstream Gene

RefSeqID: NM_001191130

[0199] Gene name: VGLL3
Product: transcription cofactor vestigial-like protein 3
Translation start: 34657637

Translation end: 34707554 Distance to

[0200] region end: 1566965 Exons: 4

[0201] 5.3.4 Repeats

Repeat name: HERVL74-int Repeat class:

LTR

[0202] Repeat family: ERVL Repeat start:
33090536

Repeat end: 33090930

[0203] 6 bov-jd-0006: 6:5440642-5440791; Over-Represented

[0204] 6.1 Sequence

TABLE-US-00011 (SEQ ID NO: 11) GGGTGTTGGTTCTCCTTGCAGGTCCTGGAGATACAGCCAAAGGCCCAGTT TTTGAGAGAACTCTTCCTAACTGTCTTCTTGTCTGAAACTAATGTAGAAG AGAGATTTTCACTAGTAGTAGTTTAGCTTATTTAGCCTGATTTCC ACCA C

[0205] 6.2 Sequence with 25 bp Surroundings

TABLE-US-00012 (SEQ ID NO: 12) TTTTGGCTTTGTGGGTGGTAGACATGGGTGTTGGTTCTCCTTGCAGGTCC TGGAGATACAGCCAAAGGCCCAGTTTTTGAGAGAACTCTTCCTAACTGTC TTCTTGTCTGAAACTAATGTAGAAGAGAGATTTTCACTAGTAGTAGTTTA GCTTATTTAGCCTGATTTCCACCACTTACATTCAGCAGCATGTTCATGG

[0206] 6.3 Annotation

[0207] 6.3.1 Genes

[0208] 6.3.2 Next Upstream Gene

RefSeqID: NM_001192907

[0209] Gene name: PRDM5
Product: PR domain zinc finger protein 5
Translation start: 4491174

Translation end: 4743136 Distance to

[0210] region end: 697505 Exons: 16

[0211] 6.3.3 Next Downstream Gene

RefSeqID: NM_001079796

[0212] Gene name: LOC780876
Product: MAD2 mitotic arrest deficient-like 1 (yeast)-like
Translation start: 5536134

Translation end: 5566460 Distance to

[0213] region end: 95344 Exons: 5

[0214] 6.3.4 Repeats

[0215] 7 bov-jd-0007: 14:1093166-1093354; Over-Represented

[0216] 7.1 Sequence

TABLE-US-00013 (SEQ ID NO: 13) GTTGTTTGTAATATTACTTAGGTATTTTTAACATTTTTATTGGAAAGTGA AAGTTAGTTTTGGTTGTGCTGGGTTTTCATTGCTGTGTGCAGTCTTTCCC TAGTTGCAGAGTGTGGGGGCTACTCTTTGTTTTAGGCTTTTCATTGTGGT GGCTTCTCTTGTTGCAGAGCCTGGGCTGCAGAGTGTGTG

[0217] 7.2 Sequence with 25 bp Surroundings

TABLE-US-00014 (SEQ ID NO: 14) AAATTGTCTGGTTTATATGCATAGAGTTGTTTGTAATATTACTTAGGTAT TTTTAACATTTTTATTGGAAAGTGAAAGTTAGTTTTGGTTGTGCTGGGTT TTCATTGCTGTGTGCAGTCTTTCCCTAGTTGCAGAGTGTGGGGGCTACTC TTTGTTTTAGGCTTTTCATTGTGGTGGCTTCTCTTGTTGCAGAGCCTGGG CTGCAGAGTGTGTGGGCTTCAGTAGTTGTGGCACATGG

[0218] 7.3 Annotation

[0219] 7.3.1 Genes

[0220] 7.3.2 Next Downstream Gene

RefSeqID: NM_001046153

[0221] Gene name: C14H8orf33
Product: UPF0488 protein C8orf33 homolog
Translation start: 1487365

Translation end: 1489409 Distance to

[0222] region end: 394012 Exons: 6

[0223] 7.3.3 Repeats

Repeat name: L1MD Repeat
class: LINE Repeat family: L1
Repeat start: 1092897

Repeat end: 1093218 Repeat

[0224] name: CHR-2A Repeat class:
SINE Repeat family: tRNA
Repeat start: 1093218

Repeat end: 1093482

[0225] 8 bov-jd-0008: 6:5425625-5425755; Under-Represented

[0226] 8.1 Sequence

TABLE-US-00015 (SEQ ID NO: 15) GATCTTATTCTTTGAAGTAATGTTATGAATCTTATCGGACAAAGCCAGAC TTCTTCATTTGGGAGTAGATTTGGAAGAGAACACTTGGTCTCTCAGCACT CCCCTTCTCAGGAAGGTTACAGAAACCAAAA

[0227] 8.2 Sequence with 25 bp Surroundings

TABLE-US-00016 (SEQ ID NO: 16) TTCTGACTCTGCAGTACCTAAATCAGATCTTATTCTTTGAAGTAATGTTA TGAATCTTATCGGACAAAGCCAGACTTCTTCATTTGGGAGTAGATTTGGA AGAGAACACTTGGTCTCTCAGCACTCCCCTTCTCAGGAAGGTTACAGAAA CCAAAATAAGACCTACCAGAATTGGGGTGG

[0228] 8.3 Annotation

[0229] 8.3.1 Genes

[0230] 8.3.2 Next Upstream Gene

RefSeqID: NM_001192907

[0231] Gene name: PRDM5
Product: PR domain zinc finger protein 5
Translation start: 4491174

Translation end: 4743136 Distance to

[0232] region end: 682488 Exons: 16

[0233] 8.3.3 Next Downstream Gene

RefSeqID: NM_001079796

[0234] Gene name: LOC780876
Product: MAD2 mitotic arrest deficient-like 1 (yeast)-like
Translation start: 5536134

Translation end: 5566460 Distance to

[0235] region end: 110380 Exons: 5

[0236] 8.3.4 Repeats

[0237] 9 bov-jd-0009: 1:29318042-29318377; Internal Reference Region

[0238] 9.1 Similarities

[0239] 14 bov-jd-0021: 25-36122654-36123000: 96.0%

[0240] 10 bov-jd-0010: 7-34812837-34813209: 83.6%

[0241] 9.2 Sequence

TABLE-US-00017 (SEQ ID NO: 17) GTTTGTAACCTGGGACCCTTGAGTTAATTCTTTTTCTTGTTATAGCCCAC CACACCTTTGCTCTGTAGGAATGCAACTTTATCTAATGCTTTTTTGGAGG GTGGCTCCTGACCAACCACCTTTAGAGAAAAATAAGTTTTCTGAAGAAAA GGTCTTAAAATGTTAACAGGCCTCCGGGCCAGAAGATGATGCAAATCACC TAAGCTTTTGCATATGATAAGTTTGCAGGAAGAAAGCCTGGTTTGCTGCA AGACTCGACCCCTTCCCCCATTATCCTCTATGCATAACTTAAGGTATAAA AACTACTTTGAAAAATAAAGTGCGGGCCTTGTTCAC

[0242] 9.3 Sequence with 25 bp Surroundings

TABLE-US-00018 (SEQ ID NO: 18) ATTGGTGTACCGTAGTAGCTTTAATGTTTGTAACCTGGGACCCTTGAGTT AATTCTTTTTCTTGTTATAGCCCACCACACCTTTGCTCTGTAGGAATGCA ACTTTATCTAATGCTTTTTTGGAGGGTGGCTCCTGACCAACCACCTTTAG AGAAAAATAAGTTTTCTGAAGAAAAGGTCTTAAAATGTTAACAGGCCTCC GGGCCAGAAGATGATGCAAATCACCTAAGCTTTTGCATATGATAAGTTTG CAGGAAGAAAGCCTGGTTTGCTGCAAGACTCGACCCCTTCCCCCATTATC CTCTATGCATAACTTAAGGTATAAAAACTACTTTGAAAAATAAAGTGCGG GCCTTGTTCACCGAAACTTGGTCTCACCATGTCGT

[0243] 9.4 Annotation

[0244] 9.4.1 Genes

[0245] 9.4.2 Next Upstream Gene

RefSeqID: NM_001122729

[0246] Gene name: GBE1
Product: 1,4-alpha-glucan-branching enzyme
Translation start: 28659455

Translation end: 28972472 Distance to

[0247] region end: 345569 Exons: 15

[0248] 9.4.3 Next Downstream Gene

RefSeqID: NM_001191130

[0249] Gene name: VGLL3
Product: transcription cofactor vestigial-like protein 3
Translation start: 34657637

Translation end: 34707554 Distance to

[0250] region end: 5339261 Exons: 4

[0251] 9.4.4 Repeats

Repeat name: BTLTR1 Repeat
class: LTR Repeat family:
ERVK Repeat start: 29317937

Repeat end: 29318587

[0252] 10 bov-jd-0010: 7:34812863-34813185; Internal Reference Region

[0253] 10.1 Similarities

[0254] 9 bov-jd-0009: 1-29318016-29318401: 83.6%

[0255] 14 bov-jd-0021: 25-36122654-36123000: 73.7%

[0256] 16 bov-jd-0023: 28-40139930-40140429: 75.2%

[0257] 10.2 Sequence

TABLE-US-00019 (SEQ ID NO: 19) GTGTCCCTGGCAGTGTATTGATTAATATAATTGGTGTAAGTAGTAGCTTT AATGTTTGTAACCTGGGACCCTTGAGTTAATTCTTTTTCTTGTTATAGCC CACCACACCTTTGCTCTGTAGGAATGCAACTTTATCTAATGCTTTTTTGG AGGGTGGCTCCTGACCAACCACCTTTAGAGAAAAATAAGTTTTCTGAAGA AAAGGTCTTAAAATGTTAACAGGCCTCCGGGCCAGAAGATGATGCAAATC ACCTAAGCTTTTGCATATGATAAGTTTGCAGGAAGAAAGCCTGGTTTGCT GCAAGACTCGACCCCTTCCCCCA

[0258] 10.3 Sequence with 25 bp Surroundings

TABLE-US-00020 (SEQ ID NO: 20) CTAAGTTTCCATATCCATTAGTGCTGTGTCCCTGGCAGTGTATTGATTAA TATAATTGGTGTAAGTAGTAGCTTTAATGTTTGTAACCTGGGACCCTTGA GTTAATTCTTTTTCTTGTTATAGCCCACCACACCTTTGCTCTGTAGGAAT GCAACTTTATCTAATGCTTTTTTGGAGGGTGGCTCCTGACCAACCACCTT TAGAGAAAAATAAGTTTTCTGAAGAAAAGGTCTTAAAATGTTAACAGGCC TCCGGGCCAGAAGATGATGCAAATCACCTAAGCTTTTGCATATGATAAGT TTGCAGGAAGAAAGCCTGGTTTGCTGCAAGACTCGACCCCTTCCCCCATT ATCCTTCTATGCATAACTTAAG

[0259] 10.4 Annotation

[0260] 10.4.1 Genes

[0261] 10.4.2 Next Upstream Gene

RefSeqID: NM_001076190

[0262] Gene name: FTMT
Product: ferritin, mitochondrial precursor
Translation start: 33311976

Translation end: 33313090 Distance to

[0263] region end: 1499772 Exons: 1

[0264] 10.4.3 Next Downstream Gene

RefSeqID: NM_001007809

[0265] Gene name: HSD17B4
Product: peroxisomal multifunctional enzyme type 2
Translation start: 35662598

Translation end: 35763607 Distance to

[0266] region end: 849414 Exons: 24

[0267] 10.4.4 Repeats

Repeat name: BTLTR1 Repeat
class: LTR Repeat family:
ERVK Repeat start: 34812348

Repeat end: 34813462

[0268] 11 bov-jd-0011: 3:66900607-66900863; Internal Reference Region

[0269] 11.1 Similarities

[0270] 12 bov-jd-0012: 4-12626463-12626916: 79.0%

[0271] 11.2 Sequence

TABLE-US-00021 (SEQ ID NO: 21) ACTACTTACACCAATTATATTAATCAATACACTGCCAGGGACACAGCAGG TAAGGGATATGGAAACTTAGCAGCAAACAATGGCCCAACAAGTGAAAAAC CATTCACCAATACAATTTCTAATCAATCTTGTAACTACTCAAAAGAATCT GTGTTTAGACAGTTTAGAACATCTCCTGCCTCTCACAGTTGGGAGGCTCT GAACAATCCCATGTGGCCGGAAAAACCTATTCAGGCAGGCTAGAGGATTT CCAAAGG

[0272] 11.3 Sequence with 25 bp Surroundings

TABLE-US-00022 (SEQ ID NO: 22) GTCCCAGGTTACAAACATTAAAGCTACTACTTACACCAATTATATTAATC AATACACTGCCAGGGACACAGCAGGTAAGGGATATGGAAACTTAGCAGCA AACAATGGCCCAACAAGTGAAAAACCATTCACCAATACAATTTCTAATCA ATCTTGTAACTACTCAAAAGAATCTGTGTTTAGACAGTTTAGAACATCTC CTGCCTCTCACAGTTGGGAGGCTCTGAACAATCCCATGTGGCCGGAAAAA CCTATTCAGGCAGGCTAGAGGATTTCCAAAGGAGTTTGTAGGTTAAACAC TGTCAC

[0273] 11.4 Annotation

[0274] 11.4.1 Genes

[0275] 11.4.2 Next Upstream Gene

RefSeqID: NM_001080279

[0276] Gene name: GIPC2
Product: PDZ domain-containing protein GIPC2 Translation
start: 66795565

Translation end: 66895377 Distance to

[0277] region end: 5229 Exons: 6

[0278] 11.4.3 Next Downstream Gene

RefSeqID: NM_001046503

[0279] Gene name: DNAJB4
Product: dnaJ homolog subfamily B member 4
Translation start: 66922935

Translation end: 66931502 Distance to

[0280] region end: 22073 Exons: 3

[0281] 11.4.4 Repeats

Repeat name: BTLTR1 Repeat
class: LTR Repeat family:
ERVK Repeat start: 66900561

Repeat end: 66901198

[0282] 12 bov-jd-0012: 4:12626489-12626892; Internal Reference Region

[0283] 12.1 Similarities

[0284] 11 bov-jd-0011: 3-66900581-66900887: 79.0%

[0285] 17 bov-jd-0024: 8-61277849-61278098: 70.0%

[0286] 12.2 Sequence

TABLE-US-00023 (SEQ ID NO: 23) CATCATCTTCTGGCCCGGAGGCCTGTTAACATTTTAAGACCTTTTCTTCA GAAAACTTATTTTTCTCTAAAGGTGGTTGGTCAGGAGCCACCCTCCAAAA AAGCATTAGATAAAGTTGCATTCCTACAGAGCAAAGGTGTGGTGGGCTAT AACAAGAAAAAGAATTAACTCAAGGGTCCCAGGTTACAAACATTAAAGCT ACTACTTACACCAATTATATTAATCAATACACTGCCAGGGACACAGCAGG TAAGGGATATGGAAACTTAGCAGCAAACAATGGCCCAACAAGTGAAAAAC CATTCACCAATACAATTTCTAATCAATCTTGTAACTCCTCAAAAGAATCT GTGTTTAGACAGTTTAGAACATCTCCTGCCTCTCACAGTTGGGAGGCTCT GAAC

[0287] 12.3 Sequence with 25 bp Surroundings

TABLE-US-00024 (SEQ ID NO: 24) NNNNNNNAAAAGCTTAGGTGATTTGCATCATCTTCTGGCCCGGAGGCCTG TTAACATTTTAAGACCTTTTCTTCAGAAAACTTATTTTTCTCTAAAGGTG GTTGGTCAGGAGCCACCCTCCAAAAAAGCATTAGATAAAGTTGCATTCCT ACAGAGCAAAGGTGTGGTGGGCTATAACAAGAAAAAGAATTAACTCAAGG GTCCCAGGTTACAAACATTAAAGCTACTACTTACACCAATTATATTAATC AATACACTGCCAGGGACACAGCAGGTAAGGGATATGGAAACTTAGCAGCA AACAATGGCCCAACAAGTGAAAAACCATTCACCAATACAATTTCTAATCA ATCTTGTAACTCCTCAAAAGAATCTGTGTTTAGACAGTTTAGAACATCTC CTGCCTCTCACAGTTGGGAGGCTCTGAACAATCACATGTGGCCGGAAAAA CCT

[0288] 12.4 Annotation

[0289] 12.4.1 Genes

RefSeqID: NM_001192864

[0290] Gene name: ASB4
Product: ankyrin repeat and SOCS box protein 4
Translation start: 12597837

Translation end: 12699701

Exons: 5

[0291] 12.4.2 Next Upstream Gene

RefSeqID: NM_001013588

[0292] Gene name: PON2
Product: serum paraoxonase/arylesterase 2 precursor
Translation start: 12493205

Translation end: 12520270 Distance to

[0293] region end: 106218 Exons: 9

[0294] 12.4.3 Next Downstream Gene

RefSeqID: NM_001101883

[0295] Gene name: PDK4
Product: pyruvate dehydrogenase kinase 4
Translation start: 12754201

Translation end: 12767677 Distance to

[0296] region end: 127310 Exons: 11

[0297] 12.4.4 Repeats

Repeat name: BTLTR1 Repeat
class: LTR Repeat family:
ERVK Repeat start: 12626470

Repeat end: 12627280

[0298] 13 bov-jd-0020: 4:51996600-51996918; Internal Reference Region

[0299] 13.1 Similarities

[0300] 15 bov-jd-0022: X-30978410-30978660: 100.0%

[0301] 13.2 Sequence

TABLE-US-00025 (SEQ ID NO: 25) ACCAAGTTTCGGTGAACAAGGCCCGCACTTTATTTTTCAAAGTAGTTTTT ATACCTTAAGTTATGCATAGAGGATAATGGGGGAAGGGGTCGAGTCTTGC AGCAAACCAGGCTTTCTTCCTGCAAACTTATCATATGCAAAAGCTTAGGT GATTTGCATCATCTTCTGGCCCGGAGGCCTGTTAACATTTTAAGACCTTT TCTTCAGAAAACTTATTTTTCTCTAAAGGTGGTTGGTCAGGAGCCACCCT CCAAAAAAGCATTAGATAAAGTTGCATTCCTACAGAGCAAAGGTGTGGTG GGCTATAACAAGAAAAAGA

[0302] 13.3 Sequence with 25 bp Surroundings

TABLE-US-00026 (SEQ ID NO: 26) GTAAGAGAAAGAACGACATGGTGAGACCAAGTTTCGGTGAACAAGGCCCG CACTTTATTTTTCAAAGTAGTTTTTATACCTTAAGTTATGCATAGAGGAT AATGGGGGAAGGGGTCGAGTCTTGCAGCAAACCAGGCTTTCTTCCTGCAA ACTTATCATATGCAAAAGCTTAGGTGATTTGCATCATCTTCTGGCCCGGA GGCCTGTTAACATTTTAAGACCTTTTCTTCAGAAAACTTATTTTTCTCTA AAGGTGGTTGGTCAGGAGCCACCCTCCAAAAAAGCATTAGATAAAGTTGC ATTCCTACAGAGCAAAGGTGTGGTGGGCTATAACAAGAAAAAGANNNNNN NNNNNNNNNNNNNNNNNN

[0303] 13.4 Annotation

[0304] 13.4.1 Genes

RefSeqID: NM_001012999

[0305] Gene name: MET
Product: hepatocyte growth factor receptor precursor
Translation start: 51912650

Translation end: 52042198

Exons: 22

[0306] 13.4.2 Next Upstream Gene

RefSeqID: NM_001012998

[0307] Gene name: CAPZA2
Product: F-actin-capping protein subunit alpha-2
Translation start: 51781843

Translation end: 51836823 Distance to

[0308] region end: 159776 Exons: 10

[0309] Next downstream Gene

RefSeqID: NM_174004

[0310] Gene name: CAVI Product:
caveolin-1 Translation start:
52173109

Translation end: 52208687 Distance to

[0311] region end: 176192 Exons: 3

[0312] 13.4.3 Repeats

Repeat name: BTLTR1 Repeat
class: LTR Repeat family:
ERVK Repeat start: 51996400

Repeat end: 51996918

[0313] 14 bov-jd-0021: 25:36122680-36122976; Internal Reference Region

[0314] 14.1 Similarities

[0315] 9 bov-jd-0009: 1-29318016-29318401: 96.0%

[0316] 10 bov-jd-0010: 7-34812837-34813209: 73.7%

[0317] 14.2 Sequence

TABLE-US-00027 (SEQ ID NO: 27) ACACCTTTGCTCTGTAGGAATGCAACTTTATCTAATGCTTTTTTGGAGGG TGGCTCCTGACCAACCACCTTTAGAGAAAAATAAGTTTTCTGAAGAAAAG GTCTTAAAATGTTAACAGGCCTCCGGGCCAGAAGATGATGCAAATCACCT AAGCTTTTGCATATGATAAGTTTGCAGGAAGAAAGCCTGGTTTGCTGCAA GACTCGACCCCTTCCCCCATTATCCTCTATGCATAACTTAAGGTATAAAA ACTACTTTGAAAAATAAAGTGCGGGCCTTGTTCACCGAAACTTGGTC

[0318] 14.3 Sequence with 25 bp Surroundings

TABLE-US-00028 (SEQ ID NO: 28) NNNNNNNNNNNNNNNNNNNNNNNNNACACCTTTGCTCTGTAGGAATGCAA CTTTATCTAATGCTTTTTTGGAGGGTGGCTCCTGACCAACCACCTTTAGA GAAAAATAAGTTTTCTGAAGAAAAGGTCTTAAAATGTTAACAGGCCTCCG GGCCAGAAGATGATGCAAATCACCTAAGCTTTTGCATATGATAAGTTTGC AGGAAGAAAGCCTGGTTTGCTGCAAGACTCGACCCCTTCCCCCATTATCC TCTATGCATAACTTAAGGTATAAAAACTACTTTGAAAAATAAAGTGCGGG CCTTGTTCACCGAAACTTGGTCTCACCATGTCGTTCTTTCTCTTAC

[0319] 14.4 Annotation

[0320] 14.4.1 Genes

[0321] 14.4.2 Next Upstream Gene

RefSeqID: NM_001193255

[0322] Gene name: PLOD3
Product: procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 precursor Translation
start: 36057471

Translation end: 36065405 Distance to

[0323] region end: 57274 Exons: 19

[0324] 14.4.3 Next Downstream Gene

RefSeqID: NM_001077110

[0325] Gene name: AP1S1
Product: AP-1 complex subunit sigma-1A
Translation start: 36180837

Translation end: 36185662

[0326] Distance to region end: 57862 Exons: 4

[0327] 14.4.4 Repeats

Repeat name: BTSAT4 Repeat
class: Satellite Repeat family:
centr Repeat start: 36121770

Repeat end: 36124127

[0328] 15 bov-jd-0022: X:30978436-30978636; Internal Reference Region

[0329] 15.1 Similarities

[0330] 13 bov-jd-0020: 4-51996574-51996942: 100.0%

[0331] 15.2 Sequence

TABLE-US-00029 (SEQ ID NO: 29) TGCATAGAGGATAATGGGGGAAGGGGTCGAGTCTTGCAGCAAACCAGGCT TTCTTCCTGCAAACTTATCATATGCAAAAGCTTAGGTGATTTGCATCATC TTCTGGCCCGGAGGCCTGTTAACATTTTAAGACCTTTTCTTCAGAAAACT TATTTTTCTCTAAAGGTGGTTGGTCAGGAGCCACCCTCCAAAAAAGCATT A

[0332] 15.3 Sequence with 25 bp Surroundings

TABLE-US-00030 (SEQ ID NO: 30) AAAGTAGTTTTTATACCTTAAATTATGCATAGAGGATAATGGGGGAAGGG GTCGAGTCTTGCAGCAAACCAGGCTTTCTTCCTGCAAACTTATCATATGC AAAAGCTTAGGTGATTTGCATCATCTTCTGGCCCGGAGGCCTGTTAACAT TTTAAGACCTTTTCTTCAGAAAACTTATTTTTCTCTAAAGGTGGTTGGTC AGGAGCCACCCTCCAAAAAAGCATTAGCCAGAGTTGCATTCCTACAGAGC

[0333] 15.4 Annotation

[0334] 15.4.1 Genes

[0335] 15.4.2 Next Upstream Gene

RefSeqID: NM_001192150

[0336] Gene name: FMR1
Product: fragile X mental retardation protein 1 Translation
start: 30922773

Translation end: 30962111 Distance to

[0337] region end: 16324 Exons: 17

[0338] 15.4.3 Next Downstream Gene

RefSeqID: NM_001102262

[0339] Gene name: FMR1NB
Product: fragile X mental retardation 1 neighbor protein
Translation start: 30989739

Translation end: 31029260 Distance to

[0340] region end: 11104 Exons: 6

[0341] 15.4.4 Repeats

Repeat name: BTLTR1 Repeat
class: LTR Repeat family:
ERVK Repeat start: 30978173

Repeat end: 30978969

[0342] 16 bov-jd-0023: 28:40139956-40140405; Internal Reference Region

[0343] 16.1 Similarities

[0344] 28 bov-jd-0035: 27-26341465-26341714: 71.5%

[0345] 10 bov-jd-0010: 7-34812837-34813209: 75.2%

[0346] 16.2 Sequence

TABLE-US-00031 (SEQ ID NO: 31) GAAATCCTCTAGCCTGCCTGAATAGGTTTTTCCGGCCACATGGGATTGTT CAGAGCCTCCCAACTGTGAGAGGCAGGAGATGTTCTAAACTGTCTAAACA CAGATTCTTTTGAGTAGTTACAAGATTGATTAGAAATTGTATTGGTGAAT GGTTTTTCACTTCTTGGGCCATTGTTTGCTGCTAAGTTTCCATATCCCTT ACCTGCTGTGTCCCTGGCAGTGTATTGATTAATATAATTGGTGTAAGTAG TAGCTTTAATGTTTGTAACCTGGGACCCTTGAGTTAATTCTTTTTCTTGT TATAGCCCACCACACCTTTGCTCTGTAGGAATGCAACTTTATCTAATGCT TTTTTGGAGGGTGGCTCCTGACCAACCACCTTTAGAGAAAAATAAGTTTT CTGAAGAAAAGGTCTTAAAATGTTAACAGGCCTCCGGGCCAGAAGATGAT

[0347] 16.3 Sequence with 25 bp Surroundings

TABLE-US-00032 (SEQ ID NO: 32) AGTGTTTAACCTACAAACTCCTTTGGAAATCCTCTAGCCTGCCTGAATAG GTTTTTCCGGCCACATGGGATTGTTCAGAGCCTCCCAACTGTGAGAGGCA GGAGATGTTCTAAACTGTCTAAACACAGATTCTTTTGAGTAGTTACAAGA TTGATTAGAAATTGTATTGGTGAATGGTTTTTCACTTCTTGGGCCATTGT TTGCTGCTAAGTTTCCATATCCCTTACCTGCTGTGTCCCTGGCAGTGTAT TGATTAATATAATTGGTGTAAGTAGTAGCTTTAATGTTTGTAACCTGGGA CCCTTGAGTTAATTCTTTTTCTTGTTATAGCCCACCACACCTTTGCTCTG TAGGAATGCAACTTTATCTAATGCTTTTTTGGAGGGTGGCTCCTGACCAA CCACCTTTAGAGAAAAATAAGTTTTCTGAAGAAAAGGTCTTAAAATGTTA ACAGGCCTCCGGGCCAGAAGATGATGCAAATNNNNNNNNNNNNNNNNN

[0348] 16.4 Annotation

[0349] 16.4.1 Genes

[0350] 16.4.2 Next Upstream Gene

RefSeqID: NM_175775

[0351] Gene name: RGR
Product: RPE-retinal G protein-coupled receptor
Translation start: 39531570

Translation end: 39542180 Distance to

[0352] region end: 597775 Exons: 7

[0353] 16.4.3 Next Downstream Gene

RefSeqID: NM_031210

[0354] Gene name: MIR346 Product:
Translation start: 41329054

Translation end: 41329149 Distance to

[0355] region end: 1188650 Exons: 1

[0356] 16.4.4 Repeats

Repeat name: BTLTR1 Repeat
class: LTR Repeat family:
ERVK Repeat start: 40139561

Repeat end: 40140411

[0357] 17 bov-jd-0024: 8:61277875-61278074; Internal Reference Region

[0358] 17.1 Similarities

[0359] 24 bov-jd-0031: 22-42434551-42434800: 76.0%

[0360] 12 bov-jd-0012: 4-12626463-12626916: 70.0%

[0361] 17.2 Sequence

TABLE-US-00033 (SEQ ID NO: 33) ACCTTAGAACAAACCGAGGCACTATGAACATTTTGTGCTTCATGTTGATG ACTCTTAGACATGTCTACAGTAGAGGAGCAAAAACAAAACTACTAGATAT TTCATATTGACTAGTTCCCAGTTCACGGGACTCTGACATTCCCTGAGGTC AAAGTTTTCTTGTATTGGAAGCAGTTGGGTTTGCAAGGGCTGCCTTGTCT

[0362] 17.3 Sequence with 25 bp Surroundings

TABLE-US-00034 (SEQ ID NO: 34) CAGATAGAACGATATAGCAATTTTTACCTTAGAACAAACCGAGGCACTAT GAACATTTTGTGCTTCATGTTGATGACTCTTAGACATGTCTACAGTAGAG GAGCAAAAACAAAACTACTAGATATTTCATATTGACTAGTTCCCAGTTCA CGGGACTCTGACATTCCCTGAGGTCAAAGTTTTCTTGTATTGGAAGCAGT TGGGTTTGCAAGGGCTGCCTTGTCTTGAGACCATTGAAATAAGAACTCA

[0363] 17.4 Annotation

[0364] 17.4.1 Genes

[0365] 17.4.2 Next Upstream Gene

RefSeqID: NM_001111260

[0366] Gene name: MELK
Product: maternal embryonic leucine zipper kinase
Translation start: 61157468

Translation end: 61230549 Distance to

[0367] region end: 47325 Exons: 18

[0368] 17.4.3 Next Downstream Gene

RefSeqID: NM_001046100

[0369] Gene name: ZCCHC7
Product: zinc finger CCHC domain-containing protein 7
Translation start: 61611660

Translation end: 61875342 Distance to

[0370] region end: 333587 Exons: 9

[0371] 17.4.4 Repeats

[0372] 18 bov-jd-0025: 6:19804114-19804313; Internal Reference Region

[0373] 18.1 Similarities

[0374] 22 bov-jd-0029: 27-23691655-23691904: 96.0%

[0375] 28 bov-jd-0035: 27-26341465-26341714: 80.0%

[0376] 18.2 Sequence

TABLE-US-00035 (SEQ ID NO: 35) AGAAAACTTTGACCTCAGGGAATGTCAGAGTCCCGTGAACTGGGAACTAG TCAATATGAAATATCTAGTAGTTTTGTTTTTGCTCCTCTACTGTAGACAT GTCTAAGAGTCATCAACATGAAGCACAAAATGTTCATAGTGCCTCGGTTT GTTCTAAGGTAAAAATTGCTATTGCTATATCGTTCTATCTGTCACAAGCT

[0377] 18.3 Sequence with 25 bp Surroundings

TABLE-US-00036 (SEQ ID NO: 36) TGCAAACCCAACTGCTTCCAATACAAGAAAACTTTGACCTCAGGGAATGT CAGAGTCCCGTGAACTGGGAACTAGTCAATATGAAATATCTAGTAGTTTT GTTTTTGCTCCTCTACTGTAGACATGTCTAAGAGTCATCAACATGAAGCA CAAAATGTTCATAGTGCCTCGGTTTGTTCTAAGGTAAAAATTGCTATTGC TATATCGTTCTATCTGTCACAAGCTTGTCAACAAGAAAGTACCTCGAAA

[0378] 18.4 Annotation

[0379] 18.4.1 Genes

[0380] 18.4.2 Next Upstream Gene

RefSeqID: NM_001082615

[0381] Gene name: DKK2
Product: dickkopf-related protein 2 precursor
Translation start: 19381412

Translation end: 19511150 Distance to

[0382] region end: 292963 Exons: 4

[0383] 18.4.3 Next Downstream Gene

RefSeqID: NM_001035018

[0384] Gene name: AIMP1
Product: aminoacyl tRNA synthase complex-interacting multifunctional protein 1 Translation
start: 20111143

Translation end: 20138597 Distance to

[0385] region end: 306831 Exons: 7

[0386] 18.4.4 Repeats

[0387] 19 bov-jd-0026: 27:26332496-26332695; Internal Reference Region

[0388] 19.1 Similarities

[0389] 20 bov-jd-0027: 28-30011085-30011334: 95.5%

[0390] 19.2 Sequence

TABLE-US-00037 (SEQ ID NO: 37) TGGACCCCAGAAAAGAGTGTTGTGCCTAGCACAAGGTTTCTTGAGAGGTT GAACTGCCTTTGCTAATGGATTTTAAGTTTCTTTACCTCTTCCGTGATCT CTTCTAGGTTGACCTAGAAGAGAAATCTTTTGTTAGCTTTGGCTAAGTGG AGAAGTATTGCTTCACGGTGACTTGTGTGATCCTACCTGACTGTTCTAAA

[0391] 19.3 Sequence with 25 bp Surroundings

TABLE-US-00038 (SEQ ID NO: 38) TGGGATCAGGAGGTTGTAGGGAACGTGGACCCCAGAAAAGAGTGTTGTGC CTAGCACAAGGTTTCTTGAGAGGTTGAACTGCCTTTGCTAATGGATTTTA AGTTTCTTTACCTCTTCCGTGATCTCTTCTAGGTTGACCTAGAAGAGAAA TCTTTTGTTAGCTTTGGCTAAGTGGAGAAGTATTGCTTCACGGTGACTTG TGTGATCCTACCTGACTGTTCTAAACCCTTTTGATATCTATGCACTGCT

[0392] 19.4 Annotation

[0393] 19.4.1 Genes

RefSeqID: NM_001143857

[0394] Gene name: WRN
Product: Werner syndrome ATP-dependent helicase
Translation start: 26263002

Translation end: 26449795

Exons: 34

[0395] 19.4.2 Next Upstream Gene

RefSeqID: NM_001075857

[0396] Gene name: PPP2CB
Product: serine/threonine-protein phosphatase 2A catalytic subunit beta isoform Translation
start: 26041252

Translation end: 26064654 Distance to

[0397] region end: 267841 Exons: 7

[0398] 19.4.3 Next Downstream Gene

RefSeqID: NM_174128

[0399] Gene name: NRG1
Product: pro-neuregulin-1, membrane-bound isoform
Translation start: 27623937
Translation end: 27833477 Distance to region end: 1291243

Exons: 7

[0400] 19.4.4 Repeats

[0401] 20 bov-jd-0027: 28:30011111-30011310; Internal Reference Region

[0402] 20.1 Similarities

[0403] 19 bov-jd-0026: 27-26332470-26332719: 95.5%

[0404] 20.2 Sequence

TABLE-US-00039 (SEQ ID NO: 39) CAGAAAAGAATGTTGTGCCTAGCACAAGGTTTCTTGAGAGGTTGAACTGC CTTTGCTAATGGATTTTAAGTTTCTTTACCTCTTCCGTGATCTCTTCTAG GTTGACCTAGAACAGAAATCTTTTGTTAGCTTTGGCTAAGTGGAGAAGTA TTGCTTCACGGTGACTTGTGTGATCCTACCTGACTGTTCTAAACCCTTTT

[0405] 20.3 Sequence with 25 bp Surroundings

TABLE-US-00040 (SEQ ID NO: 40) GGAGGTTGTAGGGATAGTGGACCCCCAGAAAAGAATGTTGTGCCTAGCAC AAGGTTTCTTGAGAGGTTGAACTGCCTTTGCTAATGGATTTTAAGTTTCT TTACCTCTTCCGTGATCTCTTCTAGGTTGACCTAGAACAGAAATCTTTTG TTAGCTTTGGCTAAGTGGAGAAGTATTGCTTCACGGTGACTTGTGTGATC CTACCTGACTGTTCTAAACCCTTTTGATATCTATGCACTGTTGCTGCTG

[0406] 20.4 Annotation

[0407] 20.4.1 Genes

[0408] 20.4.2 Next Upstream Gene

RefSeqID: NM_174147

[0409] Gene name: PLAU
Product: urokinase-type plasminogen activator precursor
Translation start: 29964982

Translation end: 29971029 Distance to

[0410] region end: 40081 Exons: 11

[0411] 20.4.3 Next Downstream Gene

RefSeqID: NM_001191370

[0412] Gene name: VCL Product:
vinculin
Translation start: 30053805

Translation end: 30166316 Distance to

[0413] region end: 42496 Exons: 22

[0414] 20.4.4 Repeats

Repeat name: (TGC)n Repeat class:
Simple repeat Repeat family:
Simple repeat Repeat start:
30011326

Repeat end: 30011356

[0415] 21 bov-jd-0028: 4:103646990-103647189; Internal Reference Region

[0416] 21.1 Similarities

[0417] 26 bov-jd-0033: X-65494632-65494881: 85.5%

[0418] 21.2 Sequence

TABLE-US-00041 (SEQ ID NO: 41) GTATCCTGGCACATACATGTACTGCCTCACCCCTAACCTCAGTCATGTGT TCCAAGAACTTCTGTCCGTTTATTTATTTGTTTTTGGTAACATTGAATTC GTTTTGACTATGCTGGGTCTTTGCTGCTCGCTGGAAGTTGCTAGGACCTC TGGACTGCAGTCTCCCATCTCTTGCTGACCTCTTGTTGACCTCTGCAGAA

[0419] 21.3 Sequence with 25 bp Surroundings

TABLE-US-00042 (SEQ ID NO: 42) TCTACGTTAAGAGTATACTTTAAGAGTATCCTGGCACATACATGTACTGC CTCACCCCTAACCTCAGTCATGTGTTCCAAGAACTTCTGTCCGTTTATTT ATTTGTTTTTGGTAACATTGAATTCGTTTTGACTATGCTGGGTCTTTGCT GCTCGCTGGAAGTTGCTAGGACCTCTGGACTGCAGTCTCCCATCTCTTGC TGACCTCTTGTTGACCTCTGCAGAATCCTGGTTGGTGGGAGCTTGTTAG

[0420] 21.3.1 Annotation

[0421] 21.3.2 Genes

RefSeqID: NM_001193208

[0422] Gene name: UBN2 Product:
ubinuclein-2
Translation start: 103594500

Translation end: 103689157

Exons: 18

[0423] 21.3.3 Next Upstream Gene

RefSeqID: NM_001192577

[0424] Gene name: ZC3HAV1L
Product: zinc finger CCCH-type antiviral protein 1-like
Translation start: 103454360

Translation end: 103465193 Distance to

[0425] region end: 181796 Exons: 5

[0426] 21.3.4 Next Downstream Gene

RefSeqID: NM_001076997

[0427] Gene name: FMC1
Product: protein FMC1 homolog Translation start:
103715431

Translation end: 103719743 Distance to

[0428] region end: 68243 Exons: 2

[0429] 21.3.5 Repeats

Repeat name: ERV1-1C-LTR_BT Repeat class:

LTR

[0430] Repeat family: ERV1 Repeat start:
103646797

Repeat end: 103646974

[0431] 22 bov-jd-0029: 27:23691681-23691880; Internal Reference Region

[0432] 22.1 Similarities

[0433] 28 bov-jd-0035: 27-26341465-26341714: 80.5%

[0434] 18 bov-jd-0025: 6-19804088-19804337: 96.0%

[0435] 22.2 Sequence

TABLE-US-00043 (SEQ ID NO: 43) ACAAGAAAACTTTGACCTCAGGGAATGTCAGAGTCCCGTGAACTGGGAAC TAGTCAATATGAAATATCTAGTAGTTTTGTTTTTGCTCCTCTACTGTAGA CATGTCTAAGAGTCATCAACACGAAGCACAAAATGTTCATAGTGCCTCGG TTTGTTCTGAGGTAAAAATTGCTATATCGTTCTATCTGTCACAAGCTTGT

[0436] 22.3 Sequence with 25 bp Surroundings

TABLE-US-00044 (SEQ ID NO: 44) CCTTGCAAACCCAACTGCTTCCAATACAAGAAAACTTTGACCTCAGGGAA TGTCAGAGTCCCGTGAACTGGGAACTAGTCAATATGAAATATCTAGTAGT TTTGTTTTTGCTCCTCTACTGTAGACATGTCTAAGAGTCATCAACACGAA GCACAAAATGTTCATAGTGCCTCGGTTTGTTCTGAGGTAAAAATTGCTAT ATCGTTCTATCTGTCACAAGCTTGTCAACAAGAAAGTACCTCGAAAGAA

[0437] 22.4 Annotation

[0438] 22.4.1 Genes

[0439] 22.4.2 Next Upstream Gene

RefSeqID: NM_001076832

[0440] Gene name: TRMT9B
Product: probable tRNA methyltransferase 9-like protein
Translation start: 23063309

Translation end: 23137025 Distance to

[0441] region end: 554655 Exons: 6

[0442] 22.4.3 Next Downstream Gene

RefSeqID: NM_001038192

[0443] Gene name: ERI1
Product: 3-5 exoribonuclease 1
Translation start: 24193121

Translation end: 24209947 Distance to

[0444] region end: 501242 Exons: 7

[0445] 22.4.4 Repeats

[0446] 23 bov-jd-0030: 27:23723113-23723312; Internal Reference Region

[0447] 23.1 Sequence

TABLE-US-00045 (SEQ ID NO: 45) AGCCTGCCTAAATCATTGACTTCTAGCCACCTTTGGGATGCCAATGACCA CCCAGCCTTACCAGGCCACAGAGGAGAGAAAACATTTACCACATGAGGTC CGGGTAAGGAACAAGGAACTAACGAGCTCCCACCAACCAGGATTCTGCAG AGGTCAACAAGAGGTCAGCAAGAGATGGGAGACTGCAGTCCAGAGGTCCT

[0448] 23.2 Sequence with 25 bp Surroundings

TABLE-US-00046 (SEQ ID NO: 46) TTGCCTTCTCCCATATCTATTCACAAGCCTGCCTAAATCATTGACTTCTA GCCACCTTTGGGATGCCAATGACCACCCAGCCTTACCAGGCCACAGAGGA GAGAAAACATTTACCACATGAGGTCCGGGTAAGGAACAAGGAACTAACGA GCTCCCACCAACCAGGATTCTGCAGAGGTCAACAAGAGGTCAGCAAGAGA TGGGAGACTGCAGTCCAGAGGTCCTAGCAAATTCCAGCGAGCAGCTAAG

[0449] 23.3 Annotation

[0450] 23.3.1 Genes

[0451] 23.3.2 Next Upstream Gene

RefSeqID: NM_001076832

[0452] Gene name: TRMT9B
Product: probable tRNA methyltransferase 9-like protein
Translation start: 23063309

Translation end: 23137025 Distance to

[0453] region end: 586087 Exons: 6

[0454] 23.3.3 Next Downstream Gene

RefSeqID: NM_001038192

[0455] Gene name: ERI1
Product: 3-5 exoribonuclease 1
Translation start: 24193121

Translation end: 24209947 Distance to

[0456] region end: 469810 Exons: 7

[0457] 23.3.4 Repeats

Repeat name: BOV-A2 Repeat
class: SINE Repeat family: Core-RTE
Repeat start: 23722838

Repeat end: 23723098

[0458] 24 bov-jd-0031: 22:42434577-42434776; Internal Reference Region

[0459] 24.1 Similarities

[0460] 17 bov-jd-0024: 8-61277849-61278098: 76.0%

[0461] 24.2 Sequence

TABLE-US-00047 (SEQ ID NO: 47) TGACTCTTAGACATGTCTACAGTAGAGGAGCAAAAACAAAACTACTAGAT ATTTCATATTGACTAGTTCCCAGTTCACGGGACTCTGACATTCCCTGAGG TCAAAGTTTTCTTGTATTGGAAGCAGTTGGGTTTGCAAGGGCTGCCTTGT CTTGAGACCATTGAACTAAGAACTCAGAACTTGAGCACTATTATCAAAAA

[0462] 24.3 Sequence with 25 bp Surroundings

TABLE-US-00048 (SEQ ID NO: 48) ATGAACATTTTGTGCTTCATGTTGATGACTCTTAGACATGTCTACAGTAG AGGAGCAAAAACAAAACTACTAGATATTTCATATTGACTAGTTCCCAGTT CACGGGACTCTGACATTCCCTGAGGTCAAAGTTTTCTTGTATTGGAAGCA GTTGGGTTTGCAAGGGCTGCCTTGTCTTGAGACCATTGAACTAAGAACTC AGAACTTGAGCACTATTATCAAAAATCACAAGGCTCACACTGACACAGA

[0463] 24.4 Annotation

[0464] 24.4.1 Genes

[0465] 24.4.2 Next Upstream Gene

RefSeqID: NM_001040646

[0466] Gene name: FHIT
Product: bis(5-adenosyl)-triphosphatase Translation
start: 40603978

Translation end: 42134601 Distance to

[0467] region end: 299975 Exons: 9

[0468] 24.4.3 Next Downstream Gene

RefSeqID: NM_001083488

[0469] Gene name: FAM107A Product:

protein FAM107A Translation
start: 43354327

Translation end: 43359047 Distance to

[0470] region end: 919552 Exons: 4

[0471] 24.4.4 Repeats

[0472] 25 bov-jd-0032: 20:2742-294; Internal Reference Region

[0473] 25.1 Sequence

TABLE-US-00049 (SEQ ID NO: 49) TTGGGTGTCACAGTGGAGGTGTAGAAGAGGTCTGAGAGTGCAAGGCAGTT AAGGAAGAAGTACATGGGCTGGGTGATTAGCTGACTGCATGTAATAGAAA TCACAATGATCAAATTCCCCAACCAAATAGCCAGGTAACAGAATAAGAAA AATAAAAAGCAGAGGATCTGGACTTTCTTGTCCATAGAAAGTTCTAAGAG

[0474] 25.2 Sequence with 25 bp Surroundings

TABLE-US-00050 (SEQ ID NO: 50) CTCCATCAGTAAGTCAGTCATGAGTTTGGGTGTCACAGTGGAGGTGTAGA AGAGGTCTGAGAGTGCAAGGCAGTTAAGGAAGAAGTACATGGGCTGGGTG ATTAGCTGACTGCATGTAATAGAAATCACAATGATCAAATTCCCCAACCA AATAGCCAGGTAACAGAATAAGAAAAATAAAAAGCAGAGGATCTGGACTT TCTTGTCCATAGAAAGTTCTAAGAGGATAAATTCAGTAACATTATTTCT

[0475] 25.3 Annotation

[0476] 25.3.1 Genes

[0477] 25.3.2 Next Downstream Gene

RefSeqID: NM_001040540

[0478] Gene name: SPZ1
Product: spermatogenic leucine zipper protein 1 Translation
start: 153401

Translation end: 155115 Distance to

[0479] region end: 150461 Exons: 1

[0480] 25.3.3 Repeats

[0481] 26 bov-jd-0033: X:65494658-65494857; Internal Reference Region

[0482] 26.1 Similarities

[0483] 21 bov-jd-0028: 4-103646964-103647213: 85.5%

[0484] 26.2 Sequence

TABLE-US-00051 (SEQ ID NO: 51) CACCCCTAACCTCAGTCGTGTGTTCCAAGAACTTCTGTCCGTTTATTTAT TTGTTTTGGGTAACATTGAATTCGTTTTGACTATGCTGGGTCTTTGCTGC TCGCTGGAAGTTGCTAGGACCTCTGGACTGCAGTCTCCCATCTCTTGCTG ACCTCTTGTTGACCTCTGCAGAATCCTGGTTGCTGGGAGCTTGTTAGTTC

[0485] 26.3 Sequence with 25 bp Surroundings

TABLE-US-00052 (SEQ ID NO: 52) ATCCTGGCACATACATGTACTGCCTCACCCCTAACCTCAGTCGTGTGTTC CAAGAACTTCTGTCCGTTTATTTATTTGTTTTGGGTAACATTGAATTCGT TTTGACTATGCTGGGTCTTTGCTGCTCGCTGGAAGTTGCTAGGACCTCTG GACTGCAGTCTCCCATCTCTTGCTGACCTCTTGTTGACCTCTGCAGAATC CTGGTTGCTGGGAGCTTGTTAGTTCCTTGTTCCTTACCCGGACCACCTG

[0486] 26.4 Annotation

[0487] 26.4.1 Genes

[0488] 26.4.2 Next Upstream Gene

RefSeqID: NM_001166574

[0489] Gene name: TRPCS
Product: short transient receptor potential channel 5
Translation start: 65246770

Translation end: 65449919 Distance to

[0490] region end: 44738 Exons: 10

[0491] 26.4.3 Next Downstream Gene

RefSeqID: NM_031235

[0492] Gene name: MIR764 Product:
Translation start: 67800434

Translation end: 67800529 Distance to

[0493] region end: 2305578 Exons: 1

[0494] 26.4.4 Repeats

[0495] 27 bov-jd-0034: 27:26331117-26331316; Internal Reference Region

[0496] 27.1 Sequence

TABLE-US-00053 (SEQ ID NO: 53) CAAGAGGTCAGCAAGAGATGGGAGACTGCAGTCCAGAGGTCCTAGCAACT TCCAGCGAGCAGCAAAGACCCAGCATAGTCAAAACGAATTCAATGTTACC AAAAACAAATAAATAAACGGACAGAAGTTCTTGGAACACATGACTGAGGT TAGGGGTGAGGCAGTACATGTATGTGCCAGGATACTCTTAAAGTATACTC

[0497] 27.2 Sequence with 25 bp Surroundings

TABLE-US-00054 (SEQ ID NO: 54) CCAACCAGGATTCTGCAGAGGTCAACAAGAGGTCAGCAAGAGATGGGAGA CTGCAGTCCAGAGGTCCTAGCAACTTCCAGCGAGCAGCAAAGACCCAGCA TAGTCAAAACGAATTCAATGTTACCAAAAACAAATAAATAAACGGACAGA AGTTCTTGGAACACATGACTGAGGTTAGGGGTGAGGCAGTACATGTATGT GCCAGGATACTCTTAAAGTATACTCTTAACGTAGATGAGGAGAACAAGG

[0498] 27.3 Annotation

[0499] 27.3.1 Genes

RefSeqID: NM_001143857

[0500] Gene name: WRN
Product: Werner syndrome ATP-dependent helicase
Translation start: 26263002

Translation end: 26449795

Exons: 34

[0501] 27.3.2 Next Upstream Gene

RefSeqID: NM_001075857

[0502] Gene name: PPP2CB
Product: serine/threonine-protein phosphatase 2A catalytic subunit beta isoform Translation
start: 26041252

Translation end: 26064654 Distance to

[0503] region end: 266462 Exons: 7

[0504] 27.3.3 Next Downstream Gene

RefSeqID: NM_174128

[0505] Gene name: NRG1
Product: pro-neuregulin-1, membrane-bound isoform
Translation start: 27623937

Translation end: 27833477 Distance to

[0506] region end: 1292622 Exons: 7

[0507] 27.3.4 Repeats

Repeat name: ERV1-1C-LTR BT Repeat class:

LTR

[0508] Repeat family: ERV1 Repeat start:
26331316

Repeat end: 26331494

[0509] 28 bov-jd-0035: 27:26341491-26341690; Internal Reference Region

[0510] 28.1 Similarities

[0511] 22 bov-jd-0029: 27-23691655-23691904: 80.5%

[0512] 16 bov-jd-0023: 28-40139930-40140429: 71.5%

[0513] 18 bov-jd-0025: 6-19804088-19804337: 80.0%

[0514] 28.2 Sequence

TABLE-US-00055 (SEQ ID NO: 55) GACAAGGCAGCCCTTGCAAACCCAACTGCTTCCAATACAAGAAAACTTTG ACCTCAGGGAATGTCAGAGTCCCGTGAACTGGGAACTAGTCAATATGAAA TATCTGGTAGTTTTGTTTTTGCTCCTCTACTGTAGACATGTCTAAGAGTC ATCAACATGAAGCACAAAATGTTCATAGTGCCTCGGTTTGTTCTAAGGTA

[0515] 28.3 Sequence with 25 bp Surroundings

TABLE-US-00056 (SEQ ID NO: 56) TGAGTTCTTATTTCAATGGTCTCAAGACAAGGCAGCCCTTGCAAACCCAA CTGCTTCCAATACAAGAAAACTTTGACCTCAGGGAATGTCAGAGTCCCGT GAACTGGGAACTAGTCAATATGAAATATCTGGTAGTTTTGTTTTTGCTCC TCTACTGTAGACATGTCTAAGAGTCATCAACATGAAGCACAAAATGTTCA TAGTGCCTCGGTTTGTTCTAAGGTAAAAATTGCTATATCGTTCTATCTG

[0516] 28.4 Annotation

[0517] 28.4.1 Genes

RefSeqID: NM_001143857

[0518] Gene name: WRN
Product: Werner syndrome ATP-dependent helicase
Translation start: 26263002

Translation end: 26449795

Exons: 34

[0519] 28.4.2 Next Upstream Gene

RefSeqID: NM_001075857

[0520] Gene name: PPP2CB
Product: serine/threonine-protein phosphatase 2A catalytic subunit beta isoform Translation
start: 26041252

Translation end: 26064654 Distance to

[0521] region end: 276836 Exons: 7

[0522] 28.4.3 Next Downstream Gene

RefSeqID: NM_174128

[0523] Gene name: NRG1
Product: pro-neuregulin-1, membrane-bound isoform Translation start: 27623937

Translation end: 27833477 Distance to

[0524] region end: 1282248 Exons: 7

[0525] 28.4.4 Repeats

Sequence J139 (Over-Represented)

[0526]

TABLE-US-00057 (SEQ ID NO: 134) GAGTATTCCTCTGTCTCTTCATCTTGTTTAAATTGGAATCACAGATAAAT AGCCTGGAGACAAGGATTGAGAAGATGCAAGAAAGGTTTAACAAGGACCT AGAAGAAATAAAAAAGAGTCAATATATAATGAATAATGCAATAAATGACA TTAAAAACACTCTGGAGGCAACAAATAGTAGAATAACAGAGGCAGAAGAT AGGATTAGTGAATTAGAAGATAGAATGGTAGAAATAAATG

Location

Assembly Bos_taurus_UMD_3.1.1

[0527] chr22:50,204,119-50,204,340

Annotation

RepeatMasker Information

Name: L1 BT

Family: L1

Class: LINE

Sequence J141 (Over-Represented)

[0528]

TABLE-US-00058 (SEQ ID NO: 135) ATGGCACCCAGCCTTACCAGGCCACAGAGGAGAGAAAACACTTAACCACA GGTGGTCCGGGTAAGGAACAAGGAACTAACAAGCTCCCAGCAACCAGGAT TCTGCAGAGGTCAACAAGAGGTCAGCAAGAGATGGGAGACTGCAGTCCAG AGGTCCTAGCAACTTCCAGCGAGCAGCAAAGACCCACTAACCC

Location

Assembly Bos_taurus_UMD_3.1.1

[0529] chrX:65,494,744-65,494,925

Annotation

RepeatMasker Information

Sequence J143 (Over-Represented)

[0530]

TABLE-US-00059 (SEQ ID NO: 136) GTTTGGGTTGTGTTGTTAGTTCCTTGTTCCTTACCCGGACCACCTGTGGT TAAGTGTTTTCTCTCCTCTGTGGCCTGGTAAGGCTGGGTGGTCATTGGCA TCCCAAAGGTGGCTAGAGGTCAATGATTTAGGCAGGCTTGTGAATAGATA TGGGAGAAGGCAATGGCACCCCACTCCAGTACTCTTGCCTGGAAAATCCC ATGGACCCAAGAGCCTGGTAGGCTGCAGTCCATGGGGTCACTAGGAGT

Location

Assembly Bos_taurus_UMD_3.1.1

[0531] chr27:23,716,727-23,716,953

Annotation

RepeatMasker Information

Name: BOV-A2

Family: Core-RTE

Class: SINE

Sequence J145 (Over-Represented)

[0532]

TABLE-US-00060 (SEQ ID NO: 137) ACATGGAGAAGAGAAGAGGGAGGAGGGAGTTAGAAACTTTTCATCTTTAA CGTAGATGTTTTATCAATGGTGCTGTATAGAAGGAGAAGTTTTGAAACTA CTGTAAAAATAAGACCGATAACCGGAAGCAGGAGACTTAAGTCCAAACCC TGACTCCAGGGAACTCCTGACTCCAAGGAACATTAATTGACGGGAGCTCA TCAAATGCATCCATACCGACACTGAAACAAAGCACCACACAAGGGCCAAT AAATTCCAG

Location

Assembly Bos_taurus_UMD_3.1.1

[0533] chr26:5,229,059-5,229,286

Annotation

RepeatMasker Information

Name: L1 BT

Family: L1

Class: LINE

Sequence J146 (Over-Represented)

[0534]

TABLE-US-00061 (SEQ ID NO: 138) GTCTCCTGTAGACAACATATGTAGGGGTCTTGTTTTTGTATCCATTCAGC CAGTCTTTGTCTTTTGGTTGGGGCATTCAACCCATTTACGTTTAAGGTAA TTACTGATAAGTATGATCCCGTTGCCATTTACTTTATTGTTTGGGGTTCG AATTTATACACCATTTTTGTGTTTCCTGTCTAGAGAATATCCTTTAGTAT TTGTTGGAGAGCTGGTTTGGTGGTGCAGAATTCTCTCAGCTTTTGCTTGT CTGAGAAGCTTTTGATTTCTCCTTCATACTTGAATGAGATCC

Location

Assembly Bos_taurus_UMD_3.1.1

[0535] chr6:19,478,840-19,479,435

Annotation

Genes

RefSeq: NM_001082615.1

[0536] Description: Bos taurus dickkopf WNT signaling pathway inhibitor 2 (DKK2), mRNA.

Gene Symbol: DKK2

Repeats

Name: L1 BT

Family: L1

Class: LINE

Sequence J147 (Over-Represented)

[0537]

TABLE-US-00062 (SEQ ID NO: 139) GTATAACCCCGTGAACATCTCTGAGTGGTCCAGTTGTGGAGTGCACATAA GGAAGTGACTACTGGCTAGCCCACTCTCTCCACTATTGATTCACCTCATC TCATTTGGGTCACCTCTAACTCCCTCCTCCCTCTTCTCTTCTCCATGTAA CCCTGTGAACCTCTCTGAGTGACCCTCACTGTAGAGAAACTTATCATCTT TAATGTAGATGTTTTATCAATGGTGCTGTATAGAAG

Location

Assembly Bos_taurus_UMD_3.1.1

[0538] chr9:90,778,334-90,778,569

Annotation

Repeats

Name: L1 BT

Family: L1

Class: LINE

Sequence J148 (Over-Represented)

[0539]

TABLE-US-00063 (SEQ ID NO: 140) ATTCTATCTTCTAATTCACTAATCCTATCTTCTGCCTCTGTTATTCTACT ATTTGTTGCCTCCAGAGTGTTTTTAATTTCATTTATTGCATTATTCATTA TATATTGACTCTCTTTTATTTCTTCTAGGTCCTTGTTAAACCTTTCTTGC ATCTTCTCGATCTTAGTCTCCAAGCTATTTATCTGTGATTCCATTTTGAT TTCAAGATTTTGGATCAATTTCACTATCATTATAGGGAATCTACCTGATA AAGAATTCCAAATAA

Location

Assembly Bos_taurus_UMD_3.1.1

[0540] chr5:91,534,317-91,534,549

Annotation

Repeats

Name: L1 BT

Family: L1

Class: LINE

Sequence J149 (Over-Represented)

[0541]

TABLE-US-00064 (SEQ ID NO: 141) ATTTTATCTGATATGAGTATTGCTACTCCGGCTCTCCAACAAATACTAAA GGATATTCTCTAGACAGGAAACACAAAAAGGGTGTATAAATTCGAACCCA AAACAATAAAGTAAATGGCAACGGGATCATACTTATCAATAATTACCTTA AACGTAAATGGGTTGAATGCCCCAACCAAAAGACAAAGACTGGCTGAATG GATACAAAAACAAGACCCCTACATATGTTGTCTACAAGAGACCCACTTCA GACCTAGGGAC

Location

Assembly Bos_taurus_UMD_3.1.1

[0542] chr1:35,411,734-35,411,952

Annotation

Repeats

Name: L1M2

Family: L1

Class: LINE

Sequence J150 (Over-Represented)

[0543]

TABLE-US-00065 (SEQ ID NO: 142) CTTCTATACAGCACCATTGATAAAACATCTACGTTAAAGATGAACAGTTT CTCTACTGTGAGGGTCACCCAGAGAGGTTCACAGCGTTACATGGAGAAGA GAAGAGGGAGGAGGGAGTTAGAGGTGACCCGAATGAGATGAGGTGGAATC AATAGTGGAGTGAGTGGACTAGCCAATAATCACTTCCTTATGTGCACTCC ACAACTGGACCGCTCATAGATGTTCACAGAGTTATACAG

Location

Assembly Bos_taurus_UMD_3.1.1

[0544] chr6:5,515,497-5,515,735

Annotation

Repeats

Name: L1 BT

Family: L1

Class: LINE

Sequence J151 (Over-Represented)

[0545]

TABLE-US-00066 (SEQ ID NO: 143) GTTTCACATTGTCCCAGAGGTCTCTGAGGTTGTCCTAATTTCTTATAATT CTTTTTCCTTGTTTCCTCTCTGCTTCATTTATTTCTACCATTCTATCTTC TACCTCACTTATCCTATCTTCTGCCTCTGTTATTCTACTATTTGTTGCCT CCAGAGTGTTTTTAATTTCATTTATTGCATTATTCATTATATATTGACTC TTTTTTATTTCTTCTAGGTCCTTGTTAAACCTTTCTTGCATCTTCTC

Location

Assembly Bos_taurus_UMD_3.1.1

[0546] chr6:5,833,268-5,833,514

Annotation

Repeats

Name: L1-3 BT

Family: L1

Class: LINE

Sequence J153 (Over-Represented)

[0547]

TABLE-US-00067 (SEQ ID NO: 144) GTTTGGGTTTGTTGTTTGATTAATATGTGTCTTGGGGTGTTTCCCCTTGG GTTTATCCTGTTTGGGACTCTCTGGTTTTCTTGGACTTGGGTGATTATTT CCTTCCCCATTTTAGGGAAGTTTTCAACTATTATCTCCTCAAGTATTTTC TCATGGTCTTTCTTTTTGTCTTCTTCTTCTGGGACCCCTATGATTCGAAT GTTGTAGCGTTTAATATTGTCCTGGAGGTCTCTGAGATTGTCCTCATTTC TTTTAATTCGTTTTTCTTTTATTTTCTC

Location

Assembly Bos_taurus_UMD_3.1.1

[0548] chr23:1,113,953-1,114,617

Annotation

Repeats

Name: L1 BT

Family: L1

Class: LINE

Sequence JC83 (Under-Represented)

[0549]

TABLE-US-00068 (SEQ ID NO: 145) TTCCTGTGGTCATGTATGGATGTGAGAGTTGGACTGTGAAGAAGGCTGAG CGCCGAAGAATTGATGCTTTTGAACTGTGGTGTTGGAGAAGACTCTAGAG AGTCCCTTGGACTGCAAGGAGATCCAACCAGTCCATCCTAAAGGAGATCA GTCCTGCGTGTTGATTGGAAGGAATGATGCTAAAGCTGAAACTCCAGTAC TTTGACCACACA

Location

Assembly Bos_taurus_UMD_3.1.1

[0550] chr8:34,607,129-34,607,338

Annotation

Repeats

Name: BovB

Family: RTE-BovB

Class: LINE

Sequence JC86 (Under-Represented)

[0551]

TABLE-US-00069 (SEQ ID NO: 146) TTTCAAATGAGTCAGCTCTTCGCATCAGGTGGACAAAATATTGGAGTTTC AGCTTCAACATCAGGACTGATTTCCTTTAGAATGGACTGGTTGGATCTCC TTGCAGTCCAAGGGACTCTCAAGAGTCTTCTCCAACACCACAGTTCAAAA GCATCAATTCTTCAGCACTCAGCTTTCTTCACAGTCCAACTCTCACATCC AT

Location

Assembly Bos_taurus_UMD_3.1.1

[0552] chr11:60,951,570-61,196,616

Annotation

Repeats

Name: BovB

Family: RTE-BovB

Class: LINE

Sequence JC88 (Under-Represented)

[0553]

TABLE-US-00070 (SEQ ID NO: 147) GATGTGAGAGTTGGACTGTGAAGAAGGCTGAGCGCCGAAGAATTGATGCT TTTGAACTGTGGTGTTGGAGAAGACTCTTGAGAGTCCTTTGGACTGCAAG GAGATCCAACCAGTCCATTCTAAAGGAGATCAGCCCTGGGATTCCTTTGG AGGGAATGATGCTAAAGCTGAAACTCCAATACTTTGGCCACCTGATGCAA AGAAC

Location

Assembly Bos_taurus_UMD_3.1.1

[0554] chr15:44,835,477-44,836,082

Annotation

Repeats

Name: Bov-tA3

[0555] Family: tRNA-Core-RTE

Class: SINE

Name: BovB

Family: RTE-BovB

Class: LINE

Sequence JC89 (Under-Represented)

[0556]

TABLE-US-00071 (SEQ ID NO: 148) GTATAGATGTGAGAGTTGGACTGTGAAGAAGGCTGAGTGCTGAAGAATTG ATGCTTTTGAACTGTGGTGTTGGAGAAGACTCTTGAGAGTCCCTTGGACT GCAAGGAGATCCAACCAGTCCATTCTAAAGGAGGTCAGTCCTGGGTGTTC ATTGGAAGGAATGATGCTAAAGCTGAAACTCCAGTACTTTGGCCACACAA AAAACCAAACA

Location

Assembly Bos_taurus_UMD_3.1.1

[0557] chr13:33,526,513-33,526,708

Annotation

Repeats

Name: BovB

Family: RTE-BovB

Class: LINE

Sequence JC90 (Under-Represented)

[0558]

TABLE-US-00072 (SEQ ID NO: 149) GATAGCATATTAAAAATCAGAGACATTACTTTGCTGACAAAGGTTCATCT AGTTAAGGCTATGGTTTTTCCAGTAGTCATGTATGGAATTGAGAATTGCA GTATAAAGAAAGCTGAGCACCGAAGAATTGATGCTTTTGAACTGTGGTGT TGGAGAAGACTCTTGAGAGTCCCTTGGACTGCAAGGAGATCCAACCAGTC CATTCTGAAGGAGATCAGCCCTGGGATTTCTTTGGGAG

Location

Assembly Bos_taurus_UMD_3.1.1

[0559] chr29:20,418,647-20,418,884

Annotation

Genes

RefSeq: NM_001102336.1

[0560] Description: Bos taurus leucine zipper protein 2 (LUZP2), mRNA.

Gene Symbol: LUZP2

Repeats

Name: BovB

Family: RTE-BovB

Class: LINE

Sequence JC91 (Under-Represented)

[0561]

TABLE-US-00073 (SEQ ID NO: 150) CAGGACTGGAAAAGGTCAGTTTTCATTCCAATCCCAAAGAAAGGCAATGC CAAAGAATGCTCAAACTACCGCACAATTGTACTCATCTCACATGCTAGTA AAGTAATGCTCAAAATTCTCCAGGCCAGGCTTCAGCAATATGTGAACCAT GAACTTCCTGATGTTAAAGGCAGAAGAACCAGAGATCAAATTGCCAACAT CCACTGGATCATAAAAAAAGCAAGAGAGTTCCAGAAAAGCATC

Location

Assembly Bos_taurus_UMD_3.1.1

[0562] chr15:49,580,120-49,580,362

Annotation

Repeats

Name: BovB

Family: RTE-BovB

Class: LINE

Sequence JC92 (Under-Represented)

[0563]

TABLE-US-00074 (SEQIDNO:151) GTGCAATTGTGCGGTAGTTTGAGCATTCTTTGGCATTGCCTTTCTTTGGG ATTGGAATGAAAACTGACCTTTTCCAGTCCTGTGGCCACTGCTGAGTTTC CAAATTTGCTGGCATATTGAGTGCAGCACTTTCATAGCATCATCTTTTAG GATTTGAAATAGCTCACCTGGAACTCCATCACCTCCGCTACCTTTGTTTG TAGTGATGCTTCCTAAAGCCCACTTGACTTCACATTCCAGGATGTCTGGA TCTAGGTGAG

Location

Assembly Bos_taurus_UMD_3.1.1

[0564] chr2:103,004,793-103,005,045

Annotation

Repeats

Name: BTLTR1

Family: ERVK

Class: LTR

Name: BovB

Family: RTE-BovB

Class: LINE

Sequence JC93 (Under-Represented)

[0565]

TABLE-US-00075 (SEQIDNO:152) CAAATATATTGAGTCTTTTAACCACCATCTCCATAAATGGCATTAAATCC ACCAGTATTGGATTCCAGCTGAGTTATTTCAAATCCTAGAAGATGATGCT GTGAAACTGCTGCACTCAATATGCCAGCAAATTTGGAAAACTCAGCAGTG GCCACAGGACTGGAAAAGGTCAGTTTTCATTCCAATCCCAAAGAAAGGCA ATGCCAAAGAATGCTCAAACTACTGCACAATTGCACT

Location

Assembly Bos_taurus_UMD_3.1.1

[0566] chr2:3,084,175-3,084,409

Annotation

Repeats

Name: BTLTR1

Family: ERVK

Class: LTR

Name: BovB

Family: RTE-BovB

Class: LINE

Sequence JC94 (Under-Represented)

[0567]

TABLE-US-00076 (SEQIDNO:153) GATCTCCTTTAGGATGGACTGGTTGGATCTCCTTGCAGAACAAGGGACTC TCGAGTCTTTTCCAACACCGCAGTTCAAAAGCATCAATTCTTTGGCACTC AGCTTTCTTTATAGTTCAACTCTCACATCCATACATGACCACTGGAAAAA CCATAGCCTTGACTAGACGGACCTTTATTGACAAAGTAATGTCTCTGCTT TTGAATATGCTGTCTAGGTTGGTCATAACTTTCCTTCCAAGGAGTAAGTG TCTTTTAATTTCATGGCTGCAGTCACCATCTGCAGTGAT

Location

Assembly Bos_taurus_UMD_3.1.1

[0568] chr8:26,316,238-26,316,595

Annotation

Repeats

Name: BovB

Family: RTE-BovB

Class: LINE

Sequence JC95 (Under-Represented)

[0569]

TABLE-US-00077 (SEQIDNO:154) ATCCAACGGATGTTGGCAATTTGATCTCTGGTTCCTCTGCCTTTTCTAAA GCCAGCTTGAACATCTGGAAGTTCAGATTCACGTACTGCTGAAGCCTGGC TTGGAGAATTCTGAGCATTACTTTACTAGCGTGTGAAGTGAATGCAATTG TGCGGTAGTTTGAGCATTCTTTGGCATTGCCTTTCTTTGGGATTGGAATG AAAACTGACCTTTTCCAGTCCTGTGGCCACTGCTGAGTTTTCCAAATTTG CTGGCATATTGAGTGC

Location

Assembly Bos_taurus_UMD_3.1.1

[0570] chr29:27,463,561-27,463,826

Annotation

Repeats

Name: BovB

Family: RTE-BovB

Class: LINE

Sequence JC96 (Under-Represented)

[0571]

TABLE-US-00078 (SEQIDNO:155) GCATCATCTTTCAGGATTTGGAATAGGTCAGTTTTCATTCCAATCCCAAA GAAAGGCAATGCCAAAGAATGCTCAAACTACTGCACAATTGCACTCATCT CACACGCTAGTAAAGTAATGCTCAAAATTCTCCAAGCCAGGCTTCAGCAA TATGTGAACCGTGAACTTCCTGATGTTCAAGCTGGCAGGGGAACCAGAGA TCAAATTGCCAACATCCGCTGGATCATGGAAAAAGCAGAGAGTTCCAGAA AAACATCTATTTC

Location

Assembly Bos_taurus_UMD_3.1.1

[0572] chr17:56,918,088-56,918,338

Annotation

Genes

RefSeq: NM_001075763.2

[0573] Description: Bos taurus coiled-coil domain containing 63 (CCDC63), mRNA.

Gene Symbol: CCDC63

Repeats

Name: BovB

Family: RTE-BovB

Class: LINE

Sequence JC98 (Under-Represented)

[0574]

TABLE-US-00079 (SEQIDNO:156) AGTACAGCCACTATGGAGAACAGCGTGGAGATTCCTTAAAAAACTGGAAA TAGAACTGCCTTATGATCCAGCAATCCCACTGCTGGGCATACACACTGAG GAAACCAGAAGGGAAAGAGACACGTGTACCCCAATGTTCATTGCAGCACT GTTCCAGGACATGGAAGCAACCTAGATGTCCATCAGCAGATGAATGGATA AGAAAGCTGTGGTACATATATACAA

Location

Assembly Bos_taurus_UMD_3.1.1

[0575] chr2:34,160,472-34,160,696

Annotation

Repeats

Name: L1 BT

Family: L1

Class: LINE

Sequence S49 (Over-Represented)

[0576]

TABLE-US-00080 (SEQIDNO:157) GTACCCATTTTTTACTAGAGAGCGAGATTACTGGCTTGACTGCTCTCTCC CCCTTTGGACTCTCCTTTTTCTCCACCAGGTCGTCTGTGTCTCCTCCCTA ACCCCTCTCTACTTTACCCAACTCTGTGAATTTCTGTGTGTTCCAGATGG TGGGGAACACTTAGGGAACTGATTACTGGCTGGATCTGTCTCCCTTCTTT

Location

Assembly Bos_taurus_UMD_3.1.1

[0577] chr10:22,785,125-22,785,324

Annotation

Repeats

Name: L1 BT

Family: L1

Class: LINE

Sequence S53 (Over-Represented)

[0578]

TABLE-US-00081 (SEQIDNO:158) ATCGCAGCACTGTTTATAATAGCCAGGACATGGAAGCAACCTAGATGTCC ATCAGCAGATGAATGGATAAGAAAGCTGTGGTACATATACACAATGGAGT ATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGG ATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAAAAAAAAAC

Location

Assembly Bos_taurus_UMD_3.1.1

[0579] chr24:29,814,601-29,814,800

Annotation

Repeats

Name: L1 BT

Family: L1

Class: LINE

Name: BTLTR1

Family: ERVK

Class: LTR

Sequence S54 (Over-Represented)

[0580]

TABLE-US-00082 (SEQIDNO:159) TTTTCCATGCAAATAGGGACCAAAAGAAAGCAGGAGTAGCAATACTCATA TCAGATAAAATAGACTTTAAAACAAAGGCTGTGAAAAGAGACAAAGAAGG TCACTACATAATGATTAAAGGATCAATCCAAGAAGAAGATATAACAATTA TAAATATATATGCACCCAACACGGGAGCACCGCAGTATGTAAGACAAATG

Location

Assembly Bos_taurus_UMD_3.1.1

[0581] chr1:22,612,199-22,612,398

Annotation

Repeats

Name: L1 BT

Family: L1

Class: LINE

Sequence S55 (Over-Represented)

[0582]

TABLE-US-00083 (SEQIDNO:160) CTAGGGATCTCTTCAAGGAAATCAGAGATACCAAAGGAAGATTTCATGCA AAGATGAGCTCGATAAAGGACAAAAATGGTATGGACCTAACAGACGCAGA ATATATTAAGAAGAGATGGCAACAATACACAGAAGAATCATACAAAAAAG GTCTTCACGACCCAGATAATCACGATGGTGTGATCACTGACCTAGAGCCA

Location

Assembly Bos_taurus_UMD_3.1.1

[0583] chr10:99,151,264-99,151,463

Annotation

Repeats

Name: BovB

Family: RTE-BovB

Class: LINE

Sequence SC3 (Under-Represented)

[0584]

TABLE-US-00084 (SEQIDNO:161) GCATCGTTCGGAAAAAACCCCAGGTTCCAAATACAGCTCGACAAGCGGCC TCTCTCCCCGGGGACATCTCGAGAGGCAAGCGGAGCTCCATGCCTCAACC CAAGACGAGGCCTGACTCTCCTGTCCCCAGTCTGCAGGGACCCTGCGATC GGAGTCTGAAATCAGAGGTACCCTGCGGTTCCTGCCTCAACTGGAGATGA

Location

Assembly Bos_taurus_UMD_3.1.1

[0585] chr3:82,757,239-82,757,438

Annotation

Repeats

Name: BTSAT4

[0586] Family: centr

Class: Satellite

Sequence SC5 (Under-Represented)

[0587]

TABLE-US-00085 (SEQIDNO:162) AGGTGGGAGGGGCCTCTCGGGACTTTTGGGGGTTTGGTGCATTGGAAGAG GGCCTCATCTCCAGTTGAGGCAGGAACCGCAGGGTACCTCTGATTTCAGA CTCCGATCGCAGGGTCCCTGCAGACTGGGGACGGGAGAGTCAGGCCTCGT CTTGGGTTGAGGCATGGGACTCCGCTTGCCTCTCGAGATGTCCCCGGGGA

Location

Assembly Bos_taurus_UMD_3.1.1

[0588] chr1:45,727,925-45,728,124

Annotation

Repeats

Name: BTSAT4

[0589] Family: centr

Class: Satellite

Sequence SC6 (Under-Represented)

[0590]

TABLE-US-00086 ((SEQIDNO:163) TGTTTTTATCTCACGTAATGCCATAACAAACCACTTGTGGAATCTTTGTT CCTGACTAGAGATCAAGCCCTGAACCTTTGGAGTGGGAGCACTGACTCCA AGACTATAGCCTACCAGAGAGCTAACCCCAGGGAGTATCAAATAGCGGGA ACTCACACAAAGGAAAGCACTTGAAAAGGACCCAGCGTCACCCGCCGCCA

Location

Assembly Bos_taurus_UMD_3.1.1

[0591] chr24:62,416,051-62,416,250

Annotation

Repeats

Name: L1-3 BT

Family: L1

Class: LINE

Sequence SC7 (Under-Represented)

[0592]

TABLE-US-00087 (SEQIDNO:164) TCAACACGAAGGGGCAGTGACCCGCCCGTGCATCGTCCGGAAAAGACCCC CAGGTTCCAAATACAGCTCGACAAGTGGCCTCTCTCCCCGGGGACACCTC GAGAGGCAAGCGGAGTTCCATGCCTCAACCCAAGACGAGGCCTGACTCTC CTGTCCCCAGTCTGCAGGGACCCTGCGATCGGAGTCTGAAATCAGAGGAA

Location

Assembly Bos_taurus_UMD_3.1.1

[0593] chr9:45,016,883-45,017,082

Annotation

Repeats

Name: BTSAT4

[0594] Family: centr

Class: Satellite

[0595] All publications mentioned herein are hereby incorporated by reference in their entireties. While the foregoing invention has been described in some detail for purposes of clarity and understanding, it will be appreciated by one skilled in the art, from a reading of the disclosure, that various changes in form and detail can be made without departing from the true scope of the invention in the appended claims.

[0596] Specific examples of methods and kits have been described herein for purposes of illustration. These are only examples. The technology provided herein can be applied to systems other than the example systems described above. Many alterations, modifications, additions, omissions, and permutations are possible within the practice of this invention. This invention includes variations on described embodiments that would be apparent to the skilled addressee, including variations obtained by: replacing features, elements and/or acts with equivalent features, elements and/or acts; mixing and matching of features, elements and/or acts from different embodiments; combining features, elements and/or acts from embodiments as described herein with features, elements and/or acts of other technology; and/or omitting combining features, elements and/or acts from described embodiments.

[0597] The embodiments of the invention described above are intended to be exemplary only. Those skilled in this art will understand that various modifications of detail may be made to these embodiments, all of which come within the scope of the invention.

APPENDIX

[0598]

TABLE-US-00088 TABLE1 MarkerID MarkerName(internal) Assembly GenomicRegion Sequence fwdprimersequence revprimersequence bov-jd-0001 J6 UMD3.1.1 Chromosome TACCATGGTGACCACGGGTGACGGGGAAT GGAATCAGGGTT GGTCGGGA 25: CAGGGTTCGATTCCGGAGAGGGAGCCTGA CGATTCCG(SEQID GTGGGTAA 32377622-32377759 GAAACGGCTACCACATCCAAGGAAGGCAG NO:64) TTTG(SEQ CAGGCGCGCAAATTACCCACTCCCGACCC IDNO:65) GGGGAGGTAGTGACGAAAAATA(SEQID NO:1) bov-jd-0002 J7 UMD3.1.1 Chromosome GCTATCCTGAGGGAAACTTCGGAGGGAAC GGTCGGACGACC ACCCGAAA 18: CAGCTACTAGATGGTTCGATTAGTCTTTCG GATTTG(SEQID GATGGTGA 58238154-58238329 CCCCTATACCCAGGTCGGACGACCGATTTG NO:66) ACTATG CACGTCAGGACCGCTACGGACCTCCACCA (SEQIDNO: GAGTTTCCTCTGGCTTCGCCCTGCCCAGGC 67) ATAGTTCACCATCTTTCGGGTCCTAACA (SEQIDNO:3) bov-jd-0003 J8 UMD3.1.1 Chromosome TTCGCTGGATAGTAGGTAGGGACAGTGGG GACAGTGGGAAT GTAAACGG X: AATCTCGTTCATCCATTCATGCGCGTCACT CTCGTTCATC(SEQ CGGGAGTA 62078561-62078748 AATTAGATGACGAGGCATTTGGCTACCTTA IDNO:68) ACTATG AGAGAGTCATAGTTACTCCCGCCGTTTACC (SEQIDNO: CGCGCTTCATTGAATTTCTTCACTTTGACAT 69) TCAGAGCACTGGGCAGAAATCACATCGCG TCAACACCC(SEQIDNO:5) bov-jd-0004 J13 UMD3.1.1 Chromosome AGATGGATTTAGAGTGTGTGGCTGTTGTG TCTGAGTAGTCCT GTAGGTGG 21: TGTGGTTCAGAATTCTGAGTAGTCCTTTCA TTCAGGGAT(SEQ CTCGTATTA 2014523-2014688 GGGATCACCCAAAAGCTCAGACAAAGCGT IDNO:70) TCTTTCT GAGCCCTTCACGTGGACTGTGCTGTGCGT (SEQIDNO: CAGAAAGATAATACGAGCCACCTACACAA 71) TCTAAAATTTCCTAAAAACC(SEQIDNO: 7) bov-jd-0005 J14 UMD3.1.1 Chromosome AGCTGAAGTGGTGGGATAGTGTAGTTTGT GTGGTGGGATAG CACAGTCTT 1: GTGTCATAGGAATCTCCTCAAAGGATGAT TGTAGTTTGT(SEQ TGAAGGCA 33090510-33090673 GTCATCAGTGTGAGGTCCTAATTGTGTCCT IDNO:72) ACATT(SEQ AGAAAAAGTTAGAGCTGGTGAAAATGTTG IDNO:73) CCTTCAAAGACTGTGTGAGATGGCAGGTG TGGACACTGGCCCCACTG(SEQIDNO:9) bov-jd-0006 J16 UMD3.1.1 Chromosome GGGTGTTGGTTCTCCTTGCAGGTCCTGGA CTTGCAGGTCCTG CTCTCTTCT 6: GATACAGCCAAAGGCCCAGTTTTTGAGAG GAGATA(SEQID ACATTAGTT 5440642-5440791 AACTCTTCCTAACTGTCTTCTTGTCTGAAAC NO:74) TCAGACA TAATGTAGAAGAGAGATTTTCACTAGTAG (SEQIDNO: TAGTTTAGCTTATTTAGCCTGATTTCCACCA 75) C(SEQIDNO:11) bov-jd-0007 J17 UMD3.1.1 Chromosome GTTGTTTGTAATATTACTTAGGTATTTTTAA TCATTGCTGTGTG AGGCTCTG 14: CATTTTTATTGGAAAGTGAAAGTTAGTTTT CAGTCT(SEQID CAACAAGA 1093166-1093354 GGTTGTGCTGGGTTTTCATTGCTGTGTGCA NO:76) GAAG(SEQ GTCTTTCCCTAGTTGCAGAGTGTGGGGGC IDNO:77) TACTCTTTGTTTTAGGCTTTTCATTGTGGTG GCTTCTCTTGTTGCAGAGCCTGGGCTGCA GAGTGTGTG(SEQIDNO:13) bov-jd-0008 Control1 UMD3.1.1 Chromosome GATCTTATTCTTTGAAGTAATGTTATGAAT TCTTATCGGACAA TGGTTTCTG 6: CTTATCGGACAAAGCCAGACTTCTTCATTT AGCCAGAC(SEQ TAACCTTCC 5425625-5425755 GGGAGTAGATTTGGAAGAGAACACTTGGT IDNO:78) TGAG(SEQ CTCAGCACTCCCCTTCTCAGGAAGGTTA IDNO:79) CAGAAACCAAAA(SEQIDNO:15) bov-jd-0009 Universal UMD3.1.1 Chromosome GTTTGTAACCTGGGACCCTTGAGTTAATTC CTCCTGACCAACC GGCTTTCTT JU1 1: TTTTTCTTGTTATAGCCCACCACACCTTTGC ACCTTTAG(SEQID CCTGCAAA 29318042-29318377 TCTGTAGGAATGCAACTTTATCTAATGCTT NO:80) CTTATC TTTTGGAGGGTGGCTCCTGACCAACCACCT (SEQIDNO: TTAGAGAAAAATAAGTTTTCTGAAGAAAA 81) GGTCTTAAAATGTTAACAGGCCTCCGGGC CAGAAGATGATGCAAATCACCTAAGCTTTT GCATATGATAAGTTTGCAGGAAGAAAGCC TGGTTTGCTGCAAGACTCGACCCCTTCCCC CATTATCCTCTATGCATAACTTAAGGTATA AAAACTACTTTGAAAAATAAAGTGCGGGC CTTGTTCAC(SEQIDNO:17) bov-jd-0010 Universal UMD3.1.1 Chromosome GTGTCCCTGGCAGTGTATTGATTAATATAA GTCCCTGGCAGTG CAAAGGTG JU2 7: TTGGTGTAAGTAGTAGCTTTAATGTTTGTA TATTGATT(SEQID TGGTGGGC 34812863-34813185 ACCTGGGACCCTTGAGTTAATTCTTTTTCTT NO:82) TATAA(SEQ GTTATAGCCCACCACACCTTTGCTCTGTAG IDNO:83) GAATGCAACTTTATCTAATGCTTTTTTGGA GGGTGGCTCCTGACCAACCACCTTTAGAG AAAAATAAGTTTTCTGAAGAAAAGGTCTT AAAATGTTAACAGGCCTCCGGGCCAGAAG ATGATGCAAATCACCTAAGCTTTTGCATAT GATAAGTTTGCAGGAAGAAAGCCTGGTTT GCTGCAAGACTCGACCCCTTCCCCCA(SEQ IDNO:19) bov-jd-0011 Universal UMD3.1.1 Chromosome ACTACTTACACCAATTATATTAATCAATAC GTTTAGAACATCT ATCCTCTAG JU3 3: ACTGCCAGGGACACAGCAGGTAAGGGAT CCTGCCTCTC(SEQ CCTGCCTGA 66900607-66900863 ATGGAAACTTAGCAGCAAACAATGGCCCA IDNO:84) ATA(SEQID ACAAGTGAAAAACCATTCACCAATACAATT NO:85) TCTAATCAATCTTGTAACTACTCAAAAGAA TCTGTGTTTAGACAGTTTAGAACATCTCCT GCCTCTCACAGTTGGGAGGCTCTGAACAA TCCCATGTGGCCGGAAAAACCTATTCAGG CAGGCTAGAGGATTTCCAAAGG(SEQID NO:21) bov-jd-0012 Universal UMD3.1.1 Chromosome CATCATCTTCTGGCCCGGAGGCCTGTTAAC CAAAGGTGTGGT GTCCCTGG JU4 4: ATTTTAAGACCTTTTCTTCAGAAAACTTATT GGGCTATAA(SEQ CAGTGTATT 12626489-1262.6892 TTTCTCTAAAGGTGGTTGGTCAGGAGCCA IDNO:86) GATT(SEQ CCCTCCAAAAAAGCATTAGATAAAGTTGC IDNO:87) ATTCCTACAGAGCAAAGGTGTGGTGGGCT ATAACAAGAAAAAGAATTAACTCAAGGGT CCCAGGTTACAAACATTAAAGCTACTACTT ACACCAATTATATTAATCAATACACTGCCA GGGACACAGCAGGTAAGGGATATGGAAA CTTAGCAGCAAACAATGGCCCAACAAGTG AAAAACCATTCACCAATACAATTTCTAATC AATCTTGTAACTCCTCAAAAGAATCTGTGT TTAGACAGTTTAGAACATCTCCTGCCTCTC ACAGTTGGGAGGCTCTGAAC(SEQIDNO: 23) bov-jd-0013 S13 Btau4.6.1 Chromosome TCGCTGGAGGTTGCTAGGACCTCTGGACT GCTTGTTAGTTCC CTCTAGCCA 6: GCAGTCTCCCATCTCTTGCTGACCTCTTGTT TTGTTCCTTAC CCTTTGGG 6320256-6320455 GACCTCTGCAGAATCCTGGTTGCTGGGAG (SEQIDNO:88) ATG(SEQID CTTGTTAGTTCCTTGTTCCTTACCCGGACCA NO:89) CCTGTGGTTAAGTGTTTTCTCTCCTCTGTG GCCTGGTAAGGCTGGGTGGTCATTGGCAT CCCAAAGGTGGCTAGAGGTCA(SEQID NO:57) bov-jd-0014 S14 Btau4.6.1 Chromosome CATATCTATTCACAAGCCTGCCTAAATCAT CGGGTAAGGAAC CATCTCTTG 14: TGACCTCTAGCCACCTTTGGGATGCCAATG AAGGAACTAA CTGACCTCT 53324225-53324424 ACCACCCAGCCTTACCAGGCCACAGAGGA (SEQIDNO:90) TGT(SEQID GAGAAAACACTTAACCACAGGTGGTCCGG NO:91) GTAAGGAACAAGGAACTAACAAGCTCCCA GCAACCAGGATTCTGCAGAGGTCAACAAG AGGTCAGCAAGAGATGGGAGACTG(SEQ IDNO:58) bov-jd-0015 S16 Btau4.6.1 Chromosome GAAACAGGAAGCCCAGAGGTGCCCCTGTA CCTTAGGAGGTCA GAACATCC 6: GTTTGGCGAAGGCCTTAGGAGGTCACTTG CTTGGAAAT(SEQ ATGCAAAG 6338951-6339151 GAAATGCCGCTGTCTGTGAGGGGGGGAG IDNO:92) GACAAG GGGGCACATGTGCACAGAGCTGTGCAGG (SEQIDNO: CTTGTCCTTTGCATGGATGTTCTTTGTAGA 93) AATCCACCTCGGAGCCATCTCCTGATGTGT AAGAATTTCCCAGACAAACCTTGAGCT (SEQIDNO:59) bov-jd-0016 S17 Btau4.6.1 Chromosome GGGTGTGTGTGTGTGGGGGGGGGAGCCC GAGCCCTTCTTTC TTCACCCAC 7: TTCTTTCCATTCCACATGAGACCCAGTGGA CATTCCA(SEQID ATTACCGTT 62628006-62628205 CAATCCAGGCCCTGCCCACTGCATTGAGTG NO:94) GATA(SEQ TGCAGCAACAATATCAACGGTAATGTGGG IDNO:95) TGAACAACATGTATTCCTGGAATCCACTCC GTTGGCTACTGACTGTGTGTGGTGGTGGT CTGGAACCTAGACCTGGAAGCTTT(SEQID NO:60) bov-jd-0017 S18 Btau4.6.1 Chromosome GTTTATCTAAAAGCTCATATCACATTTAATT CCTGTTCTTTCGA CATAGTGC 26: TTTCGTTTTGTTCCTGTTCTTTCGAGGTACT GGTACTTTCT(SEQ CTCGGTTTG 15253287-15253486 TTCTTGTTGACAAGCTTGTGACAGATAGAA IDNO:96) TTCTA(SEQ CGATATAGCAATTTTTACCTTAGAACAAAC IDNO:97) CGAGGCACTATGAACATTTTGTGCTTCATG TTGATGACTCTTAGACATGTCTACAGTAGA GGAGCAAAAACAAAACTA(SEQIDNO: 61) bov-jd-0018 S19 Btau4.6.1 Chromosome GATACTCGCCAGCTGAGCCGCGCGACACC ACATCTGCCCGCT CTCAGCTG 6: TGCATGCTCATCTGCCTGATACTCGCCAGC CATC(SEQIDNO: GCGAGTAT 76185750-76186050 TGAGCCGCGCGACATCTGCCCGCTCATCA 98) CAG(SEQID GCCTGATACTCGCCAGCTGAGCCCCGCGA NO:99) CACCTGCCCGCTCATCAGCCTGATACTCGC CAGCTGAGCCCCGCGACACCTGCCCGCTC ATCTGCCTGATACTCGCCAGCTGAGCCGC GCGACACCTGCCCGCTCATCTGCCTGATAC TCGCCAGCTGAGCCGCGCGACACCTGCCC GCTCATCTGCCTGATACTCTCCAGGTGAAT CGCGCCA(SEQIDNO:62) bov-jd-0019 S20 Btau4.6.1 Chromosome CGACCGGAAGGTCGGGAACCCCTTGCAGA AAACCTCAGGGTT CCACAATTG 25: CAAAGCAGGGGAGTCGACCCTCCCGTCCA CCTCTC(SEQID GAGGTCGA 37331550-37331750 GATCAGGAGGGGAGAAAGGGCTCAGAGG NO:100) AAG(SEQID AGGGGGTGCCGGAAAACCTCAGGGTTCCT NO:101) CTCGAGGGAGACCGGGATTTCGGGGAACT TTGTGGGTCGCATCAAGGGTGCCAAGTGC CCTTTCGACCTCCAATTGTGGCTTCTTG (SEQIDNO:63) bov-jd-0020 Universal UMD3.1.1 Chromosome ACCAAGTTTCGGTGAACAAGGCCCGCACT AACAAGGCCCGC GCATATGA JU5 4: TTATTTTTCAAAGTAGTTTTTATACCTTAAG ACTTTA(SEQID TAAGTTTGC 51996600-51996918 TTATGCATAGAGGATAATGGGGGAAGGG NO:102) AGGAAGAA GTCGAGTCTTGCAGCAAACCAGGCTTTCTT (SEQIDNO: CCTGCAAACTTATCATATGCAAAAGCTTAG 103) GTGATTTGCATCATCTTCTGGCCCGGAGGC CTGTTAACATTTTAAGACCTTTTCTTCAGAA AACTTATTTTTCTCTAAAGGTGGTTGGTCA GGAGCCACCCTCCAAAAAAGCATTAGATA AAGTTGCATTCCTACAGAGCAAAGGTGTG GTGGGCTATAACAAGAAAAAGA(SEQID NO:25) bov-jd-0021 Universal UMD3.1.1 Chromosome ACACCTTTGCTCTGTAGGAATGCAACTTTA GCCAGAAGATGA CTTAAGTTA JU6 25: TCTAATGCTTTTTTGGAGGGTGGCTCCTGA TGCAAATCAC TGCATAGA 36122680-36122976 CCAACCACCTTTAGAGAAAAATAAGTTTTC (SEQIDNO:104) GGATAATG TGAAGAAAAGGTCTTAAAATGTTAACAGG GG(SEQID CCTCCGGGCCAGAAGATGATGCAAATCAC NO:105) CTAAGCTTTTGCATATGATAAGTTTGCAGG AAGAAAGCCTGGTTTGCTGCAAGACTCGA CCCCTTCCCCCATTATCCTCTATGCATAACT TAAGGTATAAAAACTACTTTGAAAAATAA AGTGCGGGCCTTGTTCACCGAAACTTGGT C(SEQIDNO:27) bov-jd-0022 Universal UMD3.1.1 Chromosome TGCATAGAGGATAATGGGGGAAGGGGTC GCTTAGGTGATTT TTTGGAGG JU7 X: GAGTCTTGCAGCAAACCAGGCTTTCTTCCT GCATCATCTTC GTGGCTCCT 30978436-30978636 GCAAACTTATCATATGCAAAAGCTTAGGT (SEQIDNO:106) (SEQIDNO: GATTTGCATCATCTTCTGGCCCGGAGGCCT 107) GTTAACATTTTAAGACCTTTTCTTCAGAAA ACTTATTTTTCTCTAAAGGTGGTTGGTCAG GAGCCACCCTCCAAAAAAGCATTA(SEQID NO:29) bov-jd-0023 Universal UMD3.1.1 Chromosome GAAATCCTCTAGCCTGCCTGAATAGGTTTT GTCCCTGGCAGTG CAAAGGTG JU8 28: TCCGGCCACATGGGATTGTTCAGAGCCTCC TATTGATT(SEQID TGGTGGGC 40139956-40140405 CAACTGTGAGAGGCAGGAGATGTTCTAAA NO:108) TATAA(SEQ CTGTCTAAACACAGATTCTTTTGAGTAGTT IDNO:109) ACAAGATTGATTAGAAATTGTATTGGTGA ATGGTTTTTCACTTCTTGGGCCATTGTTTGC TGCTAAGTTTCCATATCCCTTACCTGCTGT GTCCCTGGCAGTGTATTGATTAATATAATT GGTGTAAGTAGTAGCTTTAATGTTTGTAAC CTGGGACCCTTGAGTTAATTCTTTTTCTTGT TATAGCCCACCACACCTTTGCTCTGTAGGA ATGCAACTTTATCTAATGCTTTTTTGGAGG GTGGCTCCTGACCAACCACCTTTAGAGAA AAATAAGTTTTCTGAAGAAAAGGTCTTAA AATGTTAACAGGCCTCCGGGCCAGAAGAT GAT(SEQIDNO:31) bov-jd-0024 Universal UMD3.1.1 Chromosome ACCTTAGAACAAACCGAGGCACTATGAAC ATTGACTAGTTCC AGCCCTTGC SU1 8: ATTTTGTGCTTCATGTTGATGACTCTTAGA CAGTTCACG(SEQ AAACCCAA 61277875-61278074 CATGTCTACAGTAGAGGAGCAAAAACAAA IDNO:110) (SEQIDNO: ACTACTAGATATTTCATATTGACTAGTTCCC 111) AGTTCACGGGACTCTGACATTCCCTGAGGT CAAAGTTTTCTTGTATTGGAAGCAGTTGGG TTTGCAAGGGCTGCCTTGTCT(SEQIDNO: 33) bov-jd-0025 Universal UMD3.1.1 Chromosome AGAAAACTTTGACCTCAGGGAATGTCAGA GAGTCATCAACAT AGCTTGTG SU2 6: GTCCCGTGAACTGGGAACTAGTCAATATG GAAGCACAA(SEQ ACAGATAG 19804114-19804313 AAATATCTAGTAGTTTTGTTTTTGCTCCTCT IDNO:112) AACGATA ACTGTAGACATGTCTAAGAGTCATCAACAT (SEQIDNO: GAAGCACAAAATGTTCATAGTGCCTCGGT 113) TTGTTCTAAGGTAAAAATTGCTATTGCTAT ATCGTTCTATCTGTCACAAGCT(SEQID NO:35) bov-jd-0026 Universal UMD3.1.1 Chromosome TGGACCCCAGAAAAGAGTGTTGTGCCTAG CTTCCGTGATCTC GTCAGGTA SU3 27: CACAAGGTTTCTTGAGAGGTTGAACTGCCT TTCTAGGTTG GGATCACA 26332496-26332695 TTGCTAATGGATTTTAAGTTTCTTTACCTCT (SEQIDNO:114) CAAGTC TCCGTGATCTCTTCTAGGTTGACCTAGAAG (SEQIDNO: AGAAATCTTTTGTTAGCTTTGGCTAAGTGG 115) AGAAGTATTGCTTCACGGTGACTTGTGTG ATCCTACCTGACTGTTCTAAA(SEQIDNO: 37) bov-jd-0027 Universal UMD3.1.1 Chromosome CAGAAAAGAATGTTGTGCCTAGCACAAGG AGGTTGACCTAGA GGGTTTAG SU4 28: TTTCTTGAGAGGTTGAACTGCCTTTGCTAA ACAGAAATCTT AACAGTCA 30011111-30011310 TGGATTTTAAGTTTCTTTACCTCTTCCGTGA (SEQIDNO:116) GGTAGG TCTCTTCTAGGTTGACCTAGAACAGAAATC (SEQIDNO: TTTTGTTAGCTTTGGCTAAGTGGAGAAGTA 117) TTGCTTCACGGTGACTTGTGTGATCCTACC TGACTGTTCTAAACCCTTTT(SEQIDNO:39) bov-jd-0028 Universal UMD3.1.1 Chromosome GTATCCTGGCACATACATGTACTGCCTC GACTATGCTGGGT TTCTGCAGA SU5 4: ACCCCTAACCTCAGTCATGTGTTCCAAGA CTTTGCT(SEQID GGTCAACA 103646990-103647189 ACTTCTGTCCGTTTATTTATTTGTTTTTGG NO:118) AGAG(SEQ TAACATTGAATTCGTTTTGACTATGCTGG IDNO:119) GTCTTTGCTGCTCGCTGGAAGTTGCTAGG ACCTCTGGACTGCAGTCTCCCATCTCTTG CTGACCTCTTGTTGACCTCTGCAGAA(SEQ IDNO:41) bov-jd-0029 Universal UMD3.1.1 Chromosome ACAAGAAAACTTTGACCTCAGGGAATGTC ACTTTGACCTCAG TGCTTCGTG SU6 27: AGAGTCCCGTGAACTGGGAACTAGTCAAT GGAATGTC(SEQ TTGATGACT 23691681-23691880 ATGAAATATCTAGTAGTTTTGTTTTTGCTCC IDNO:120) CTTA(SEQ TCTACTGTAGACATGTCTAAGAGTCATCAA IDNO:121) CACGAAGCACAAAATGTTCATAGTGCCTC GGTTTGTTCTGAGGTAAAAATTGCTATATC GTTCTATCTGTCACAAGCTTGT(SEQID NO:43) bov-jd-0030 Universal UMD3.1.1 Chromosome AGCCTGCCTAAATCATTGACTTCTAGCCAC TTGACTTCTAGCC GCTCGTTA SU7 27: CTTTGGGATGCCAATGACCACCCAGCCTTA ACCTTTGG(SEQID GTTCCTTGT 23723113-23723312 CCAGGCCACAGAGGAGAGAAAACATTTAC NO:122) TCCT(SEQ CACATGAGGTCCGGGTAAGGAACAAGGA IDNO:123) ACTAACGAGCTCCCACCAACCAGGATTCTG CAGAGGTCAACAAGAGGTCAGCAAGAGA TGGGAGACTGCAGTCCAGAGGTCCT(SEQ IDNO:45) bov-jd-0031 Universal UMD3.1.1 Chromosome TGACTCTTAGACATGTCTACAGTAGAGGA ATTGACTAGTTCC CAAACCCA SU8 22: GCAAAAACAAAACTACTAGATATTTCATAT CAGTTCACG(SEQ ACTGCTTCC 42434577-42434776 TGACTAGTTCCCAGTTCACGGGACTCTGAC IDNO:124) AATAC(SEQ ATTCCCTGAGGTCAAAGTTTTCTTGTATTG IDNO:125) GAAGCAGTTGGGTTTGCAAGGGCTGCCTT GTCTTGAGACCATTGAACTAAGAACTCAG AACTTGAGCACTATTATCAAAAA(SEQID NO:47) bov-jd-0032 Universal UMD3.1.1 Chromosome TTGGGTGTCACAGTGGAGGTGTAGAAGA CTGAGAGTGCAA TACCTGGCT SU9 20:2742-2941 GGTCTGAGAGTGCAAGGCAGTTAAGGAA GGCAGTTA(SEQ ATTTGGTTG GAAGTACATGGGCTGGGTGATTAGCTGAC IDNO:126) GG(SEQID TGCATGTAATAGAAATCACAATGATCAAAT NO:127) TCCCCAACCAAATAGCCAGGTAACAGAAT AAGAAAAATAAAAAGCAGAGGATCTGGA CTTTCTTGTCCATAGAAAGTTCTAAGAG (SEQIDNO:49) bov-jd-0033 Universal UMD3.1.1 Chromosome CACCCCTAACCTCAGTCGTGTGTTCCAAGA CTCGCTGGAAGTT CTCCCAGCA SU10 X: ACTTCTGTCCGTTTATTTATTTGTTTTGGGT GCTAGG(SEQID ACCAGGAT 65494658-65494857 AACATTGAATTCGTTTTGACTATGCTGGGT NO:128) TC(SEQID CTTTGCTGCTCGCTGGAAGTTGCTAGGACC NO:129) TCTGGACTGCAGTCTCCCATCTCTTGCTGA CCTCTTGTTGACCTCTGCAGAATCCTGGTT GCTGGGAGCTTGTTAGTTC(SEQIDNO:51) bov-jd-0034 Universal UMD3.1.1 Chromosome CAAGAGGTCAGCAAGAGATGGGAGACTG CAAGAGGTCAGC TCCAAGAA SU11 27: CAGTCCAGAGGTCCTAGCAACTTCCAGCG AAGAGATGG(SEQ CTTCTGTCC 26331117-26331316 AGCAGCAAAGACCCAGCATAGTCAAAACG IDNO:130) GTTTAT AATTCAATGTTACCAAAAACAAATAAATAA (SEQIDNO: ACGGACAGAAGTTCTTGGAACACATGACT 131) GAGGTTAGGGGTGAGGCAGTACATGTAT GTGCCAGGATACTCTTAAAGTATACTC (SEQIDNO:53) bov-jd-0035 Universal UMD3.1.1 Chromosome GACAAGGCAGCCCTTGCAAACCCAACTGC AGCCCTTGCAAAC ATTGACTA SU12 27: TTCCAATACAAGAAAACTTTGACCTCAGGG CCAA(SEQIDNO: GTTCCCAGT 26341491-26341690 AATGTCAGAGTCCCGTGAACTGGGAACTA 132) TCACG(SEQ GTCAATATGAAATATCTGGTAGTTTTGTTT IDNO:133) TTGCTCCTCTACTGTAGACATGTCTAAGAG TCATCAACATGAAGCACAAAATGTTCATAG TGCCTCGGTTTGTTCTAAGGTA(SEQID NO:55)