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