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Table 1 Features of transcriptionally active HERV-K(HML-2) loci identified in this study1.

From: Expression patterns of transcribed human endogenous retrovirus HERV-K(HML-2) loci in human tissues and the need for a HERV Transcriptome Project

 

Transcripts

ORF

             
 

gag

env

gag

env

type 1/2

5' LTR

age

band

location amplicon in genome

Hughes '04 polymorphic

Stauffer '04 ESTs

Mayer '04 Rec ORFs

Lavie '05

Buzdin '06 cDNAs

Dewannieux '06

c1_A

+

+

  

1

+

h

1p31.1

1

75616984

75617620

1p31

   

1p31.1

 

c1_B

+

+

(+)

 

1

+

h

1q22

1

153869999

153870635

 

1q22*

  

1q23.1#

 

c1_C

+

   

1

+

h

1q23.3

1

158928816

158929450

      

c3_A

+

+

  

1

+

h

3p25.3

3

9869025

9869661

      

c3_B

+

+

+

 

1

+

h

3q13.2

3

114232719

114233355

 

3q13.2*

  

3q13.2

 

c3_C

+

+

  

2

+

h

3q21.2

3

127093452

127094088

  

3q21.2

 

3q21.2

 

c3_D

+

   

2

-

h

3q24

3

149766793

149767429

      

c3_E

+

 

+

 

1

+

h

3q27.2

3

186769952

186770588

    

3q27.2

 

c4_A

+

   

1

+

och

4q32.3

4

166137900

166138546

    

4q32.1

 

c5_A

+

+

+

 

1

+

h

5q33.3

5

156024213

156024849

    

5q33.3

 

c6_A

+

+

+

+

2

+

h

6q14.1

6

78490549

78491185

K109

 

6q14.1

6q14.1

6q14.1

K109

c7_A

+

+

+

+

2

+

h

7p22.1

7

4604296

4604932

K108

 

7p22.1

7p22.1

7p22.1

K108

c7_B

+

    

-

h

7q22.1

7

104179212

104179848

    

7q22.2#

 

c7_C

+

   

OLD

-

roch

7q34

7

141100988

141101724

      

c8_A

+

   

2

+

h

8p23.1

8

7350016

7350652

K115

   

8p23

K115

c10_A

+

+

  

2

+

ch

10p14

10

6913351

6913990

 

10p14

10p14

10p14

  

c10_B

+

   

2

-

h

10q24.2

10

101576412

101577048

  

10q24.2

 

10q24.2

 

c11_A

+

+

 

+

2

+

h

11q22.1

11

101072629

101073265

11q22

 

11q22.1

11q22.1

11q22.1

 

c11_B

+

   

1

+

ch

11q23.3

11

118103837

118104468

      

c12_A

 

+

+

+

2

+

h

12q14.1

12

57014704

57015340

12q14

12q14

12q14.1

12q14.1

12q14.1

 

c19_A

 

+

   

-

h

19p13.3

19

337322

340413

      

c21_A

+

+

  

2

+

h

21q21.1

21

18861736

18862372

    

21q21.1

 

c22_A

+

+

+

 

1

+

h

22q11.21

22

17307812

17308448

    

22q11.21

 
  1. 1 Provirus designations are given in the first column. Each provirus was identified (indicated by "+") by gag- and/or env-derived cDNAs. Presence of ORFs for Gag and Env proteins was deduced from proviral sequences as given in the March 2006 version of the human genome sequence at the Human Genome Browser. The Gag ORF in provirus c1_B harbors a premature stop in the human genome reference sequence but a full-length ORF allele appears to be the more frequent allele in Caucasians (own unpublished data). Provirus type 1 or 2, based on a 292 bp sequence within the pol-env boundary (if the proviral region is present), presence of a 5'LTR. "age" indicates presence of orthologous HML-2 loci in rhesus (r), orang-utan (o), chimpanzee (c) and/or human (h) genomes, thus indicating evolutionary ages of loci. The chromosomal band in which the provirus is located, and the nucleotide position of the RT-PCR amplicon amplified during cDNA generation are given in the following columns. Locus c7_A is an HERV-K(OLD) provirus. For c19_A the position of the env amplicon is given. We compared our results with other recent publications (see text for details and references). Hughes '04 denotes proviruses that were identified as polymorphic in the human population. Stauffer '04 denotes proviruses previously identified as transcriptionally active by analysis of EST data. "*" indicates that transcriptionally activity of those proviruses was ambiguous based on EST sequence data. Mayer '04 denotes proviruses with ORFs for Rec protein. Lavie '05 denotes proviral 5'LTRs previously examined for promoter activity. Note that the 5'LTR of provirus c10_A displayed very low transcriptional activity in the previous study when in Tera-1 cells in transient reporter assays. Buzdin '06 denotes transcribed proviruses identified by means of GREM (see text). "#" indicates that a different chromosomal band was given for that locus, but sequence comparisons show that corresponding loci are identical with the loci identified in our study. Dewannieux '06 denotes proviruses reported as capable of creating an infectious HML-2 variant by recombination. See the text for above mentioned references. Note that provirus designations in other publications are different. Great care has been taken to relate provirus designations mentioned in other studies with proviruses mentioned in this study.
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BMC Genomics

ISSN: 1471-2164

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