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Table 2 The human hsp60 pseudogenes

From: Chaperonin genes on the rise: new divergent classes and intense duplication in human and other vertebrate genomes

Name1

Start2

End3

Str4

Chr5

Loc6

Ex7

P/D8

Ka/Ks9

LRT10

FS11

SC12

aa13

CCT1-1P

19,986,638

19,987,216

+

12

p12.2

1

P

0.75

0.16

5

2

190

CCT1-2P

41,621,756

41,623,646

-

5

p13.1

2?

D

1.21

0.15

7

5

512

CCT1-3P14

42,801,030

42,802,033

+

7

p14.1

3

D

0.68

2.10

1

1

367

CCT3-1P

16,177,578

16,178,178

+

8

p22

1

P

1.02

0.0

2

2

159

CCT4-1P

64,177,578

64,409,590

+

X

q12

3

D

0.65

1.76

0

3

512

CCT4-2P

140,344,301

140,345,787

-

7

q34

4

D

0.82

1.24

2

10

278

CCT5-1P14,15

78,382,086

78,382,680

+

13

q31.1

1

P

0.81

0.20

3

4

549

CCT5-2P15

78,382,866

78,382,967

-

13

q31.1

1

?

-

-

-

1

34

CCT5-3P

114,876,388

114,877,290

+

5

q22.3

1

P

0.25

2.12

6

3

201

CCT6-1P

14,692,965

14,693,954

-

5

p15.2

1

P

1.00

0.0

2

2

330

CCT6-2P

109,013,584

109,014,117

-

11

q22.3

1

P

0.90

0.0

0

2

178

CCT6-3P16

64,162,812

64,171,325

+

7

q11.21

8

D

0.43

3.06

5

4

289

CCT6-4P

191,915,332

191,916,879

+

3

q28

1

P

0.57

6.90**

9

4

292

CCT6-5P14,16

64,853,564

64,865,440

+

7

q11.21

10

D

0.84

0.34

12

6

399

CCT7-1P14

92,251,627

92,307,366

-

5

q15

1

P

0.45

1.88

3

5

145

CCT7-2P

150,242,815

150,243,240

+

6

q25.1

1

P

0.87

0.10

3

4

552

CCT8-1P14

145,141,482

145,143,137

-

1

q21.1

1

P

1.14

0.10

2

3

561

HSPD1-1P14

135,744,902

135,745,039

-

5

q31.1

1

P

1.46

0.27

0

0

48

HSPD1-2P14,17

21,919,402

21,920,175

-

5

p14.3

1

P

0.90

0.10

1

1

264

HSPD1-3P

43,602,029

43,602,280

-

20

q13.12

4

D

-

-

0

1

84

HSPD1-4P

88,065,673

88,066,269

+

6

q15

1

P

0.55

1.08

4

5

199

HSPD1-5P14

55,191,053

55,192,769

+

12

q13.2

1

P

0.56

3.08

2

1

499

HSPD1-6P14

36,783,612

36,785,195

-

3

P22.3

1

P

0.59

2.46

2

2

443

HSPD1-7P18

7,263,938

7,265,475

+

8

p23.1

1

P

1.12

0.18

5

4

396

HSPD1-8P

145,986,418

145,987,946

+

4

q31.21

1

P

0.63

2.32

4

3

458

HSPD1-9P18

7,785,932

7,787,502

-

8

p23.1

1

P

0.91

0.08

5

3

416

HSPD1-10P

8,058,884

8,082,857

+

12

p13.31

2?

D

0.78

0.94

1

1

307

HSPD1-11P

95,130,459

95,132,169

+

5

q15

5

D

0.74

2.44

6

6

375

HSPD1-12P

78,321,372

78,323,341

+

13

q31.1

1

P

0.62

4.98*

5

4

410

HSPD1-13P

153,068,626

153,068,943

+

6

q25.2

1

P

0.54

2.84

1

2

108

HSPD1-14P14

37,465,288

37,466,827

-

13

q13.3

4

D

0.68

3.3

6

3

361

HSPD1-15P

19,269,394

19,270,353

+

5

p14.3

4

D

0.74

1.24

4

4

241

HSPD1-16P

105,082,802

105,083,755

+

11

q22.3

2?

D

0.51

6.24*

5

4

199

HSPD1-17P

34,077,070

34,078,293

+

1

p35.1

3

D

0.74

1.48

2

2

217

HSPD1-18P

56,105,684

56,108,736

+

20

q13.32

5

D

0.48

10.84**

3

2

299

HSPD1-19P

50,318,868

50,319,008

+

10

q11.23

1

?

2.42

0.72

0

0

47

HSPD1-20P

78,924,341

78,924,478

-

12

q21.31

1

?

0.40

3.08

0

0

46

HSPD1-21P

60,994,430

60,994,876

-

5

q12.1

6

D

-

-

0

6

155

HSPD1-22P

29,181,851

29,183,334

-

21

q21.3

2?

D

0.69

1.4

3

4

344

  1. 1Pseudogene names follow the HUGO nomenclature. They are composed of the name of the parental gene followed by a unique number identifier and the suffix "P" (Pseudogene); 2Start and 3 End positions of the pseudogene on the chromosome; 4Strand; 5Chromosome; 6Location on the chromosome; 7Number of exons. A question mark indicates gene fragments with uncertain numbers of exons; 8Processed (P), duplicated (D) or undetermined (?); 9Ratio of non-synonymous vs. synonymous substitution rates; 10Likelihood Ratio Test (LRT) values. Values different from 1.0 with probability p < 0.01 (**) or p < 0.05 (*) are shown in bold-face; 11Number of Frame-Shifts recognized in the coding region of the pseudogene; 12Number of in-frame Stop Codons recognized in the coding region of the pseudogene; 13Length in amino acids of pseudo-translation of the recognized pseudogene sequence; 14Ten pseudogenes previously reported in the Ensembl (roman), Pseudogene.org (italics) or NCBI (bold) databases: CCT1-3P = OTTHUMG00000033751; CCT5-1P = Human.chr13.mb78; CCT6-5P = ENSP00000275603, Human.chr7.mb64; CCT7-1P = ENST00000399032; CCT8-1P = Human.chr1.mb145; HSPD1-1P = ENSG00000162241, Human.chr5.mb135; HSPD1-2P = ENSP00000328369; HSPD1-5P = LOC644745; HSPD1-6P = LOC645548; HSPD1-14P = OTTHUMG00000016753; 15,16,18Tandemly duplicated;17Previously identified as Hsp60s2 (Hsp60 short form 2).
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BMC Ecology and Evolution

ISSN: 2730-7182

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