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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.
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BMC Genomics

ISSN: 1471-2164

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