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Table 1 Relative cloning frequencies of gag amplicon-derived cDNA sequences assignable to unique HERV-K(HML-2) loci*

From: Transcriptional profiling of HERV-K(HML-2) in amyotrophic lateral sclerosis and potential implications for expression of HML-2 proteins

Locus designation ALS Ctrl Type Env [aa] Rec/Np9 hg19
motor occi sc motor occ sc
chr1p31.1_K-1 1.57 1.49   2.90 4.17 1.56 1 606 Np9 chr1:75844857
chr1q22_K-7 0.31   1.43 0.72    1 606 Np9 chr1:155603549
chr3p12.3_K-*      1.04   2 242   chr3:75601670
chr3q12.3_K-5 52.20 39.55 58.57 60.14 52.08 64.06 1 263 Np9 chr3:101412824
chr3q13.2_K-3       1.56 1 434 Np9 chr3:112750203
chr3q21.2_K-4 11.01 15.67 7.14 13.04 13.54 1.56 2   Rec chr3:125611223
chr4p16.1a_K-* 0.63    0.72 1.04   2 158   chr4:9125672
chr4p16.1b_K-* 0.31   1.43   2.08 1.56 2 342 longer chr4:9661733
chr5q33.3_K-10 1.57 5.22 5.71 0.72    1 139 (969)   chr5:156091809
chr7p22.1_K-6 0.63       2 699 (f-l) Rec chr7:4637944
chr7q22.2_K-14 0.94 1.49 2.86 2.17 1.04 3.13 del    chr7:104392150
chr7q34_K-15 8.49 9.70 8.57 9.42 10.42 4.69 del    chr7:141454695
chr8p23.1a_K-* 3.46 10.45    1.04   2 264   chr8:12081367
chr8p23.1b_K-* 5.35 2.24     7.81 2 264   chr8:12323877
chr10p14_K-16 1.89 2.99 2.86 2.17   7.81 2 286 Rec chr10:6873520
chr11q12.3_K-27 2.83 2.99   3.62 3.13 6.25 2 337   chr11:62148198
chr11q22.1_K-25 0.94       2 661   chr11:101567880
chr19q13.12_K-29 6.92 8.21 11.43 3.62 10.42   2 206   chr19:37604891
chr21q21.1_K-23 0.31    0.72    1 197 Np9 chr21:19940039
chr22q11.21_K-24 0.63       1 606 Np9 chr22:18934451
# cDNA sequences 318 134 70 138 96 64     
# samples 11 6 2 5 2 2     
  1. *Designations of HML-2 loci identified as transcribed are given in the left column. Relative cloning frequencies of cDNA sequences from the HML-2 gag amplicon assignable to either of those loci are summarized for motor cortex (motor), occipital region (occi) and spinal cord (sc) tissue samples from patients with ALS and from controls. Total numbers of cDNA sequences assigned for each tissue group and numbers of samples analyzed per tissue group are given in the two bottom lines. Detailed cloning frequencies for each sample are given in Additional file 1: Table S2. For each HML-2 locus, provirus type 1 or 2, the length of the potentially encoded Env protein in number of amino acids (see also Fig. 2) and potential coding capacity for Rec or Np9 proteins are shown in the columns that follow. Note that locus chr7p22.1_K-6 encodes a canonical full-length (f-l) Env protein of 699 aa, and locus chr5q33.3_K-10 potentially encodes an Env protein portion of approximately 139 aa, while the locus also harbors a longer Pro-Env ORF of 969 aa (see text). The rightmost column gives the chromosomal location of the respective HML-2 locus in human reference genome sequence GRCh37/hg19. For the sake of brevity, only one nucleotide position (approximately the central position of the gag amplicon) is given. Relative cloning frequencies are also depicted in Fig. 2