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Table 1 Details of HML-2 Env-encoding provirusesa

From: Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines

Provirus name

Other common names

Genome coordinates (orientation)

GenBank Accession

Percentage of population with provirusb

Provirus age (my)

Full-length ORFs

6q14.1

K109

chr6:78427019–36083(−)

AF164615

100

< 2

gag, envc

7p22.1a & bd

HML-2.HOM

K108 L & R

chr7:4622057–40031(−)

AC072054

100

< 2

a = pol, envc

b = pol, env

8p23.1a

K115

chr8:7355397–64859(−)

AY037929

15

5e

pol, envc,f

11q22.1

K118

chr11:101565794–75259(+)

N/A

78

< 2

polg

12q14.1

K119

chr12:58721242–30698(−)

AC074261

67

< 2

gag, envc

19p12b

K113

chr19:21841539h

AY037928

10–30

< 0.5

gag, pol, envc

19q11

ERVK-19

chr19:28128498–37361(−)

Y17833

100

< 5

gag, pol, envc

Xq21.33

N/A

chrX:93606603h

N/A

< 5

0.67–1.3

gag, pol, env

  1. aData including name from ref. [20]. (genome coordinates from GRCh37/hg19), unless otherwise indicated
  2. bData on proportion of individuals carrying full-length provirus taken from refs [18, 21, 22]; note, provirus 7p22.1 is polymorphic for the tandem duplication
  3. cProtein expression shown by transfection [23] (12q14.1 & 19q11 identified as K74261 & K17833 respectively in that study)
  4. dTandem duplication
  5. eLTR divergence suggests an age of 5-9my for 8p23.1a [20] but, because provirus is human-specific, the integration date must be at the lower boundary (human chimp divergence is ~5mya)
  6. fThe one nucleotide deletion in gag may be a sequencing error
  7. gAs mentioned in the main text, this provirus has a premature stop codon 38 amino acid positions before the normal terminus in env, which might not prevent expression at the cell surface
  8. hPre-integration site coordinates (Xq21.33 from ref. [18])