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Table 1 Summary of absolute numbers of np9 and rec representing cDNA sequences assignable to HERV-K(HML-2) loci a

From: HERV-K(HML-2) rec and np9 transcripts not restricted to disease but present in many normal human tissues

Type 1/2 loci

HGNC

Band

Heart

Heart tot. RNA

Brain

Brain tot. RNA

Placenta

Lung

Liver

Skeletal muscle

Kidney

Pancreas

Spleen

Thymus

Prostate

Testis

Ovary

Small intestine

Colon

Colon tot. RNA

Leukocyte

ORF

mRNA

chr1:75615359-75621731

ERVK-1

1p31.1

    

1

    

1

         

Y

np9

chr1:153863081-153872260

ERVK-7

1q22

1

7

  

11

15

21

2

1

1

22

11

4

7

 

10

8

6

24

Y

chr1:158927199-158936430

ERVK-18

1q23.3

           

3

  

1

 

1

 

2

 

chr3:102893427-102902549

ERVK-5

3q12.3

1

10

6

1

 

7

3

1

2

1

1

2

4

7

 

3

5

12

 

Y

chr3:114225814-114234972

ERVK-3

3q13.2

            

1

      

Y

chr4:166136289-166143518

-

4q32.3

             

1

      

chr22:17306187-17315361

ERVK-24

22q11.21

  

1

                

Y

HERV-K111

  

16

6

10

5

2

 

2

5

6

1

 

2

2

 

1

3

4

11

  

Venter locus

  

1

13

1

 

6

2

 

3

4

15

  

5

 

13

5

3

   

Not assignable np9-like

  

15

25

7

3

4

 

2

12

4

5

2

4

12

3

8

5

4

18

  

rec

chr2:187093879-187095344

ERVK-30

2q32.1

10

13

2

2

6

5

4

4

 

13

13

12

3

1

5

4

8

28

17

 

chr3:127091992-127101129

ERVK-4

3q21.2

   

1

           

1

 

1

 

Y

chr5:30522516-30531962

-

5p13.3

            

1

      

Y

chr5:92818136-92819668

ERVK-31

5q15

2

8

13

89

10

11

1

  

4

7

1

11

7

10

9

7

12

  

chr6:78483381-78492802

ERVK-9

6q14.1

     

1

 

15

           

Y

chr7:4588583-4606557

ERVK-6

7p22.1

     

1

      

1

   

2

  

Y

chr10:101570559-101577735

ERVK-17

10q24.2

    

1

 

8

  

1

   

3

  

1

  

Y

chr12:57007509-57016965

ERVK-21

12q14.1

 

3

  

2

1

  

20

  

1

  

1

1

1

  

Y

chr19:32820338-32829201

ERVK-27

19q12

  

2

                

Y

Total # of sequences

46

85

42

101

43

43

41

42

37

42

45

36

44

29

39

41

44

88

43

 
  1. aNormal tissue types from which cDNA sequences were generated are indicated on the top. Values in italics indicate results from experiments starting from total RNA instead of pre-made cDNA specifically for heart, brain, and colon tissue (see paper text). HML-2 loci including chromosomal coordinates in the hg18 human reference genome sequence are indicated in the left-most column, followed by HUGO Gene Nomenclature Committee (HGNC)-assigned locus designations [29] and location in chromosomal bands. Total numbers of analyzed cDNA sequences per tissue are indicated at the bottom. np9-like cDNA sequences unambiguously assignable to recently described HERV-K111 and Venter locus sequences not present in the human reference genome sequence (see text for details) are given separately. np9-like cDNA sequences not assignable to any of the listed or other HML-2 type 1 locus sequences are also given separately. Presence of ORFs for Np9 or Rec protein (‘Y’) in predicted mRNA sequences derived from the various HML-2 loci is indicated. See Figure 5 for actual protein sequences.
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