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Table 1 Results of the RACE experiment to determine the TSS of retina transcripts

From: Mapping of transcription start sites of human retina expressed genes

Gene Symbol

RACE results

TSS location

Chr.

Shape

CAGE

   

Start

Int. peak

End

   

C1orf32

Two new first exons

Isoform a

165,208,791

  

1q24.1

SP

+

  

Isoform b

165,269,346

   

-

-

 

Extension exon 0 of 180 bp

Isoform a

98,329,050

 

98,329,083

2q11.2

BR

+

CNGA3

 

Isoform b

98,329,288

   

SP

-

  

Isoform c

98,329,371

   

SP

+

DHRS3

New first exon

Isoform a

12,578,722

  

1p36.1

SP

-

 

Shorter exon 1 of 508 bp

Isoform b

12,599,903

 

12,599,935

 

SP

-

ELOVL5

New first Exon

 

53,320,946

  

6p21.1-p12.1

-

-

KIFC3

Two new first exons

Isoform a

56,437,970

  

16q13-q21

SP

-

  

Isoform b

56,370,953

   

SP

-

RCV1

Extension exon 1 of 203 bp

Isoform a

9,749,613

9,749,402

9,748,934

17p13.1

PB

-

 

New first Exon

Isoform b

9,745,910

   

-

-

 

Lack of exon 1. exon 2 extended

Isoform c

9,745,244

 

9,745,221

 

MU

-

RDH12

Two new exons

 

67,254,268

67,254,276

67,257,284

14q24.1

MU

-

  

Isoform c

19,778,103

  

9p22-p13

SP

-

SLC24A2

Two new first exons

Isoform a

19,778,808

   

-

-

  

Isoform b

19,778,609

   

-

+

  

Isoform d

19,776,949

 

19,777,002

 

PB

+

 

Lack of exon 2

 

76,839,115

 

76,839,078

6q14.2-q15

SP

-

IMPG1

Lack of exon 1. shortening exon2

 

76,808,496

   

SP

-

 

Complete in the first 3 Exons

 

76,839,060

   

-

-

SAG

Lack of exon 2

 

233,998,462

 

233,998,525

2q37.1

BR

-

AIPL1

 

61 bp

6,279,208

 

6,279,306

17p13.1

-

-

AOC2

 

10 bp

38,250,126

  

17q21

SP

+

CLUL1

 

31 bp

606,669

606,693

606,698

18p11.32

PB

-

CNGB3

 

43 bp

88,404,286

 

88,404,354

8q21-q22

-

-

EYA3

 

14 bp

28,287,732

 

28,287,684

1p36

BR

+

FSCN2

 

66 bp

77,109,947

 

77,109,997

17q25

-

-

GNAT1

 

44 bp

50,204,027

 

50,204,047

3p21

-

-

GRK7

 

40 bp

142,979,632

 

142,979,726

3q21-q23

BR

-

GUCA1B

 

19 bp

42,270,691

42,270,689-42,270,672

42,270,649

6p21.1

PB

-

GUCY2D

 

30 bp

7,846,687

  

17p13.1

-

-

HPCA

 

15 bp

33,124,670

 

33,124,680

2p25.1

MU

+

IMPDH1

 

206 bp

127,837,736

  

7q31.3-q32

SP

+

IMPG2

 

23 bp

102,522,132

 

102,522,102

3q12.2-q12.3

BR

-

LRRC21

Extension exon 1 of

121 bp

85,991,318

85,991,280

85,991,194

10q23

PB

-

MPP4

 

30 bp

202,271,692

202,271,616

202,271,601

2q33.2

PB

-

OPN4

 

67 bp

88,404,287

  

10q22

SP

-

PDC

 

17 bp

184,696,879

 

184,696,869

1q25.2

MU

-

PDE6H

 

7 bp

15,017,238

 

15,017,243

12p13

SP

-

PRPF31

 

117 bp

59,310,532

 

59,310,609

19q13.42

MU

-

RdCVF

 

37 bp

17,432,763

17,432,753-17,432,735

17,432,716

19p13.11

MU

-

RDH5

 

39 bp

54,400,449

  

12q13-q14

SP

-

RDH8

 

63 bp

9,984,862

9,984,925

9,984,991

19p13.2-p13.3

MU

-

RDS

 

61 bp

42,798,348

 

42,798,296

6p21.2-p12.3

BR

-

RLBP1

 

83 bp

87,566,008

 

87,565888

15q26

-

-

ROM1

 

215 bp

62,136,883

 

62,137,111

11q13

BR

-

RPGR

 

7 bp

38,071,739

 

38,071,704

Xp11.4

BR

-

TULP1

 

70 bp

35,588,693

 

35,588,651

6p21.3

PB

+

CRB2

 

52 bp

125,158,322

 

125,158,324

9q33.2

-

-

CRX

Shortening exon 1 of

60 bp

53,016,971

53,017,001

53,017,005

19q13.3

SP

-

RP1

 

53 bp

55,691,206

 

55,691,233

8q11-q13

BR

+

WDR17

 

77 bp

177,224,132

177,224,169-177,224,185

177,224,202

4q34

MU

+

ABCA4

  

94,359,290

 

94,359,245

1p22.1-p21

BR

-

C14ORF2

  

103,457,619

  

14q32.33

-

+

C1QL2

  

119,632,934

  

2q14.2

-

-

C7orf9

  

25,427,912

  

7p21-p15

-

-

CHM

  

85,189,194

 

85,189,222

Xq21.2

BR

+

ELOVL4

  

80,714,034

  

6q14

-

+

OPN1SW

Previous 5' end confirmed

128,203,084

  

7q31.3-q32

SP

-

RAX

  

55,091,570

  

18q21.32

SP

-

RBP3

  

48,010,989

 

48,011,000

10q11.2

-

-

RDH11

  

67,232,201

 

67,232,186

14q24.1

SP

-

RHO

  

130,730,174

  

3q21

SP

-

RPL14

  

40,473,831

  

3p22

SP

+

RS1

  

18,600,144

  

Xp22.2-p22.1

SP

-

  1. The Table provides Gene Symbols of the processed genes, RACE results referring to the RefSeq entry (database release 18), nucleotide position of the TSS (start, internal frequent start and end) referring to the UCSC Human Genome Browser (March 2006 assembly), Chromosomal location (Chr.), shape of the TSS (Shape) according to the classification of Carninci et al., 2006: single peak [SP], broad [BR], bimodal/multimodal [MU], broad with dominant peak shape [PB], comparison with Cage TSS database (+ for correspondence, – no correspondence). The genes are listed according to the type of results that was obtained according to the description in the text: (i) new TSSs within novel exons (8 genes), (ii) alternative splice form of the second exon (2 genes:, (iii) extension of the annotated first exon (27 genes), (iv) length shortening of the annotated first exon (4 genes), (v) confirmation of previously annotated TSSs (13 genes).
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BMC Genomics

ISSN: 1471-2164

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