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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.