Table 1

Summary of results from the in silico analysis of PAG genes in the bovine genome.

Gene name

PAG grouping

Transcript ID

REFSEQ number/

Temporary Gene ID

GLEAN

Chromosome

location

Comment

Missing exons


BOPAG-1

Modern

M73962

NM_174411

10324

ChrUn.13

full-length

BOPAG-2

Ancient

L06151

NM_176614

19448

Chr29.48

full-length

BOPAG-2 like

Ancient

XM_001252523

Temporary ID:786

10441

predicted; partial

Partial exon-6

BOPAG-3

Modern

XM_615231

Temporary ID:2418

24765

Chr29.54

full-length

BOPAG-4

Modern

AF020506

NM_176615

10334

ChrUn.13

full-length

BOPAG-4 like

Modern

XM_600174

24769

predicted; full length

BOPAG-5

Modern

NM_176616

18735

ChrUn.278

full-length

BOPAG-5 like

Modern

XM_001252636

Temporary ID:3317

13899

ChrUn.1071

predicted; full length

BOPAG-5 like

Modern

XM_001252636

10439

ChrUn.833

predicted; full length

BOPAG-5 like

Modern

XM_598365

10317

predicted: partial

Missing Exons 1–2

BOPAG-6

Modern

AF020508

NM_176617

24763

Chr29.54

full-length

BOPAG-7

Modern

BC133469

NR

full-length

BOPAG-7 like

Modern

NM_176618

NR

Splice variant

BOPAG-7-like

Modern

NM_001109978

13897

ChrUn.1071

predicted; partial

Missing Exon 6

BOPAG-8

Ancient

AF020510

NM_176619

24771

Chr29.54

full-length

BOPAG-9

Modern

AF020511

NM_176620

18917

ChrUn.1099

full-length

BOPAG-10

Ancient

AF020512

NM_176621

19477

Chr29.48

full-length

BOPAG-10-like

Ancient

XM_864803

Temporary ID:2428

19475

Chr29.48

predicted; partial

Misisng Exon 9

BOPAG-10-like

Ancient

XM_864803

Temporary ID:2805

19476

Chr29.48

predicted; partial

Misisng Exon 9

BOPAG-11

Ancient

AF_020513

NM_176623

24761;24762

Chr29.54

full-length

BOPAG-12

Ancient

AF_020514

NM_176622

19478

Chr29.48

full-length

BOPAG-12-like

Ancient

Temporary ID:3319

10442

ChrUn.833

predicted;partial

Partial exon 5

BOPAG-13

Ancient

AF_192330

NR

not represented

BOPAG-14

Modern

AF_192331

NR

not represented

BOPAG-15

Modern

AF_192332

NM_176624

10338

ChrUn.13

full-length

BOPAG-16

Modern

AF_192333

NM_176625

10332

ChrUn.13

full-length

BOPAG-16-like

Modern

XM_596391

Temporary ID:391

10319

ChrUn.13

predicted;full length

BOPAG-17

Modern

AF_192334

NM_176627

17225*

* Model error

BOPAG-17-like

Modern

XM_001252975

Temporary ID:2324

10321

ChrUn.13

predicted;partial

Missing exon 5

BOPAG-18

Modern

AF_192335

NM_176626

18733

ChrUn.278

full-length

BOPAG-19

Modern

AF_192336

NM_176628

10322

ChrUn.13

full-length

BOPAG-19-like

Modern

XM_001253033

Temporary ID:535

10323

ChrUn.13

predicted;full length

BOPAG-19-like

Modern

Temporary ID: 2015

10327

ChrUn.13

predicted:partial

Misisng Exon 9

BOPAG-19-like

Modern

Temporary ID:994

10328

ChrUn.13

predicted;partial

BOPAG-20

Modern

AF_192337

NM_176629

10330

ChrUn.13

full-length

BOPAG-21

Modern

AF_192338

NM_176630

10329

ChrUn.13

full-length

BOPAG-22

Modern

AY911498

NR

not represented


* Model error: The GLEAN model has an error. The displayed sequence does not match the GLEAN model sequence.

NR: GLEAN model was not represented in the bovine genome build.

Telugu et al. BMC Genomics 2009 10:185   doi:10.1186/1471-2164-10-185

Open Data