Skip to main content

Table 1 Detailed analysis for the MASA identified somatic and spermatozoal transcripts tagged with the GATA repeat motif from water buffalo Bubalus bubalis#

From: Organization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalis

(i) mRNA transcripts uncovered from different tissues
Clone ID Accession no. Tissue origin/Size(bp) Homology Status Accession no. of the homologue Gene length Chromo-somal position Position of uncovered transcripts % Homology
pJC29 DQ289479 Brain/1769 1. Bos taurus target 1 genomic scaffold DP000008 2072671 - 109–395 90%
pJC30 DQ289480 Heart/1768 2. Bos taurus lactoferrin (Lf) gene, 5' flanking region exons 1, 2 AY319306 8212 22 123–385 90%
pJC31 DQ289481 Liver/1768       
pJC32 DQ289482 Lung/1812 3. Bos taurus T-cell receptor gamma cluster 2 (TCRG2) gene AY644518 188109 - 109–386 89%
pJC33 DQ289483 Ovary/1767       
pJC34 DQ289484 Spleen/1772 4. Bos taurus prion preproprotein (PRNP) and prion-like protein doppel preproprotein gene AY944236 207929 - 131–395 90%
pJC43 DQ494486 Testis/1767       
pJC55 NS Kidney/1812 5. Bos taurus glutamate-cysteine ligase catalytic subunit (GCLC) AY957499 447010 - 109–356 91%
pJC44 DQ534902 Kidney/1303 1. Pig DNA sequence from clone CH242-277I8 CR956634 206278 17 104–277 86%
pJC45 DQ534903 Liver/1303 2. Human DNA sequence from clone RP5-1009H6 on chromosome 20 Contains the 3' end of the NFATC2 gene for cytoplasmic calcineurin-dependent (2) nuclear factor of activated T-cells HS1009H6 89163 20 158–245 90%
pJC56 NS Ovary/1303      627–774  
pJC57 NS Spleen/1303       
pJC58 NS Testis/1303       
pJC35 DQ304116 Heart/1080 1. Human DNA sequence from clone RP11-148E14 on chromosome 10 Contains part of the BTRC gene for beta-transducin repeat AL627144 36454 10 281–884 94%
pJC36 DQ304117 Liver/1080 2. Mus musculus BAC clone RP23-408K9 from chromosome 19 AC140332 206515 19 282–884 90%
pJC37 DQ304118 Lung/1080       
pJC38 DQ494481 Ovary/1080       
pJC39 DQ494482 Spleen/1080       
pJC41 DQ494484 Kidney/1080       
pJC59   Testis/1080       
pJC40 DQ494483 Testis/1043 1. Bos taurus prion protein (PRNP) and prion – like protein doppel (PRND) genes, PRNT gene, exons 1 and 2; and putative protein gene DQ205538 104027 13q17 333–857 89%
    2. Ovis aries prion protein gene U67922 31412 - 333–857 88%
    3. Odocoileus hemionus prion protein (prnp) gene AY330343 65476 - 333–857 87%
pJC42 DQ494485 Kidney/1067 1. Bos taurus similar to ring finger protein 149 (LOC506267) XM_582694 4148 - 398–597 97%
    2. Canis familiaris similar to ring finger protein 149 XM_538454 1152 10 403–446 93%
pJC46 DQ534904 Liver/848 1. B. taurus mRNA HBGF-1 for acidic fibroblast growth factor (5'end) X66446 412 - 131–441 97%
pJC60 NS Spleen/850       
pJC61 NS Heart/848 2. Bos taurus fibroblast growth factor, acidic (FGF1), mRNA NM_174055 4005 7 131–374 97%
pJC62 NS Testis/848       
pJC63 NS Kidney/848 3. Bubalus bubalis clone BBMS119 microsatellite sequence AY779568 452 - 68–285 100%
pJC64 NS Ovary/848       
pJC65 NS Lung/858 4. Homo sapiens gene for acidic fibroblast growth factor Z14150 1185 - 256–842 86%
pJC54 DQ834345 Testis/725 1. Bos taurus target 1 genomic scaffold DP000008 2072671 - 139–261 90%
    2. Bos taurus bone morphogenetic protein receptor IB gene, exons 8 and 9 AY242067 1253 6 139–261 86%
    3. Bos taurus testis expressed sequence 10, mRNA BC112672 2828 - 174–253 91%
pJC49 DQ534907 Ovary/635 1. Human DNA sequence from clone RP4-752I6 on chromosome 1 Contains the 5' end of the WASF2 gene for WAS protein family BX293535 71971 1 445–485 91%
pJC66 NS Kidney/635      555–635  
pJC67 NS Heart/635       
pJC68 NS Liver/635       
pJC69 NS Testis/647       
pJC70 NS Spleen/635       
    2. Mouse DNA sequence from clone RP23-125F21 on chromosome 4 AL627184 152069 4 555–635 90%
pJC50 DQ534908 Spleen/612 1. Bos taurus similar to ankyrin repeat domain 26 XM_580719 1470 21 119–368 86%
pJC71 NS Ovary/612       
*pJC48 DQ534906 Testis/523 1. Bos taurus similar to ankyrin repeat domain 26 XM_580719 1470 21 156–405 86%
pJC72 NS Ovary/523       
pJC47 DQ534905 Brain/455 1. Bubalus bubalis clone 2 minisatellite sequence AY230133 419 - 43–437 100%
pJC73 NS Heart/455 2. Homo sapiens 12 PAC RPCI1-53O8 AC005344 153836 12 125–251 86%
pJC74 NS Kidney/455       
pJC75 NS Ovary/455       
pJC76 NS Spleen/455       
pJC77 NS Lung/455       
pJC78 NS Testis/455       
pJC79 NS Liver/455       
pJC53 DQ834344 Heart/412 1. Bos taurus DNA for SINE sequence Bov-tA X64124 197 - 52–224 89%
    2. Bos taurus ABCG2 gene, PKD2 gene and SPP1 gene, clone RPCI42_5K14 AJ871176 171712 6 52–233 86%
    3. Bos taurus similar to ataxin-1 ubiquitin-like interacting protein, transcript variant 6 XM_882781 3406 3 54–116 87%
pJC51 DQ534909 Testis/209 1. Mus musculus chromosome 1, clone RP23-474A1 AC163217 184175 1 186–209 100%
pJC80 NS Liver/209       
pJC81 NS Lung/209 2. Mus musculus BAC clone RP24-114C10 from chromosome 13 AC165149 191162 13 188–209 100%
pJC82 NS Ovary/209       
pJC83 NS Spleen/209       
pJC84 NS Kidney/209       
pJC85 NS Heart/209       
*pJC52 DQ534910 Testis/217 1. Bos taurus similar to Ubiquitin-associated protein 1, transcript variant 2 XM_865289 4601 8 7–207 99%
    2. Canis familiaris similar to Ubiquitin-associated protein 1, transcript variant 1 XM_531976 2660 11 37–207 94%
    3. Macaca mulatta ubiquitin associated protein 1 (UBAP1), XM_001089450 4100 15 9–207 90%
    4. Homo sapiens ubiquitin associated protein 1 (UBAP1), NM_016525 2752 9p13.3 9–207 90%
(ii) mRNA transcripts identified in the spermatozoa
Clone ID Accession no. Size (bp) Homology Status Accession no. of the homologue Gene length Chromosomal position Position of uncovered transcripts % Homology
pJSC1 DQ789045 1313    ▪ Same as pJC44–45 and pJC56–58      
pJSC2 DQ789046 857    ▪ Same as pJC46 and pJC60–61      
pJSC3 DQ789047 807 1. Bubalus bubalis minisatellite associated amplified segment AY212951 757 - 16–792 96%
    2. Bos taurus similar to non-POU domain containing, octamer-binding BC105532 2580 - 558–737 90%
pJSC4 DQ789048 789 1. Hippopotamus amphibius DNA, SINE-containing sequence AB007204 311 - 582–611 100%
    2. Bos taurus BTA29 11629 genomic sequence contig containing highly polymorphic single nucleotide sites DQ404153 18838 29 659–686 100%
    3. Globicephala macrorhynchus DNA, CHR-2 SINE FL type sequence AB071578 321 - 659–742 88%
pJSC5 DQ789049 844 1. Bos taurus similar to zinc finger, DHHC domain XM_869440 1676 - 217–414 91%
    2. Canis familiaris similar to zinc finger, DHHC domain XM_846705 1470 - 290–397 83%
pJSC6 DQ834346 797 1. Homo sapiens BAC clone RP11-703G6 from 4 AC074349 176467 4 95–401 85%
pJSC7 DQ834347 840    ▪ Same as pJC48 and pJC50    -   
pJSC8 DQ845141 635    ▪ Same as pJC49 and pJC66–70    -   
pJSC9 DQ845142 507 1. Bos taurus prion preproprotein (PRNP) and prion-like protein doppel preproprotein (PRND AY944236 207929 - 52–339 88%
    2. Bos taurus T cell receptor gamma cluster 2 (TCRG2) gene AY644518 188109 - 52–339 87%
    3. Capra hircus sex-specific gonadal PISRT1 mRNA AF404302 48420 1q43 52–337 87%
pJSC10 DQ845143 516 1. Bos taurus similar to Disabled homolog 2 BC111684 805 - 272–443 97%
    2. Homo sapiens disabled-2 gene AF218839S1 2196 5p12–p13 356–507 91%
    3. Pan troglodytes similar to disabled 2 p93 XM_517792 5113 5 356–435 91%
pJSC11 DQ845144 523    ▪ Same as pJC48, pJC50 and pJSC6    -   
pJSC12 DQ845145 532 1. Human DNA sequence from clone RP11-790G19 on chromosome 10 Contains the 5' end of the gene for transmembrane receptor Unc5H2, the 3'end of a novel gene and two CpG islands AL359832 195130 10 394–431 97%
pJSC13 DQ845146 531 1. Mus musculus chromosome 15, clone RP24-236A19 AC158973 187091 15 46–327 83%
    2. Homo sapiens chromosome 8, clone RP11-1077K19 AC104247 118230 8 133–377 84%
pJSC27   522    ▪ Same as pJC48, 50, 71 & 72    -   
pJSC14 DQ904036 455    ▪ Same as pJC47 and pJC73–79    -   
pJSC15 DQ904037 392 1. Mus musculus BAC clone RP23-136L14 from chromosome 16 AC166171 199601 16 362–398 100%
pJSC16 DQ904038 387 1. B. taurus micosatellite DNA, clone BOV1.1.2 Y07736 826 - 160–335 89%
    2. Bos taurus BAC CH240-275I24 (Children's Hospital Oakland Research Institute Bovine BAC Library (male) AC150707 153353 - 120–261 90%
pJSC17 DQ904039 354 1. Bos taurus similar to Potassium voltage-gated channel subfamily C member 4 (Voltage-gated potassium channel subunit Kv3.4) (Raw3) XM_613047 2561 3 33–346 97%
pJSC18 DQ913640 267 1. Zebrafish DNA sequence from clone CH211-222O4 in linkage group 3 BX004760 190220 - 2–28 96%
pJSC19 DQ913641 277 1. Mus musculus BAC clone RP23-111N9 from chromosome 7 AC147502 202934 7 165–191 96%
pJSC20 DQ913642 291 1. Bos taurus partial ed1 gene for Ectodysplasin 1 BTA300468 9596 Xq22–q24 97–220 91%
    2. Bos taurus HIV-1 Tat interactive protein 2 HTATIP2 BC104577 1645 - 97–218 90%
    3. Bos taurus similar to C4b-binding protein alpha chain precursor (Proline-rich protein) (PRP) XM_583188 2960 - 97–216 90%
pJSC21 DQ913643 301    ▪ Same as pJC48, pJC50, pJSC6 and pJSc11    -   
pJSC22 DQ913644 273 1. Ovis aries 5' flanking region of the Jaagsiekte Sheep Retrovirus integration site AY322397 466 - 91–203 89%
    2. Bos taurus similar to NipSnap1 protein XM_866639 2458 17 100–203 90%
    3. Bos taurus lysozyme (LZ) gene U25810 12039 5q23 118–205 91%
pJSC23 DQ913645 274 1. Human DNA sequence from clone RP11-541N10 on chromosome 10 Contains the 5' end of the SH3MD1 gene for SH3 multiple domains 1, a novel gene and two CpG islands AL133355 190882 10 103–254 89%
pJC24 DQ913646 269 NA    -   
pJSC25 DQ916743 229 1. Mus musculus BAC clone RP23-476B3 from chromosome 7 AC121827 183470 7 1–26 100%
pJSC26 DQ916744 209    ▪ Same as pJC51, pJC80–85    -   
  1. # The transcripts uncovered from somatic and gonadal tissues are given in (i) whereas spermatozoal transcripts in (ii). All of the GACA-tagged transcripts were submitted to the GenBank and the accession numbers were obtained for each transcript. The analysis carried out for their homologues, size and chromosomal positions is also given. Blast search showed homology of these transcripts with several genes/gene fragments across the species. Notably, only few of them represented by '*' had homology along the length while others showed partial homology.