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Table 3 Relative cloning frequencies and locus origins of rec/np9 amplicon cDNA sequences*

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

Locus designation np9 rec Type Rec/Np9 hg19
ALS ctrl ALS ctrl
motor motor sc sc sc sc motor motor sc sc sc motor sc
32-Mot 35-Mot 357-SC 5847-SC 802-SC 5458-SC 32-Mot 35-Mot 357-SC 5847-SC 802-SC 23-Mot 5458-SC
chr3q12.3_K-5 98 5 88 86 15 33 0 0 0 0 0 0 0 1 Np9 chr3:101412824
chr3q21.2_K-4 0 16(*) 0 14 0 4(*) 0 0 0 0 0 0 25 2 Rec chr3:125611223
chr5q15_K-31 0 0 0 0 0 0 100 100 100 100 100 100 75 “2”   chr5:92793228
chr22q11.21_K-24 0 0 0 0 8 4 0 0 0 0 0 0 0 1 Np9 chr22:18934451
Venter 0 68 0 0 0 17 0 0 0 0 0 0 0 1   
HERV-K111 2 11 0 0 46 17 0 0 0 0 0 0 0 1   
ambiguous 0 0 12 0 31 25 0 0 0 0 0 0 0    
# cDNA sequences 64 19 17 7 13 24 16 18 2 1 3 23 4    
  1. *A total of 7 different ALS-derived and control samples were investigated. Percentages of cDNA sequences assignable to specific HML-2 loci are given. Relative cloning frequencies are separated into np9 and rec-typical lengths. Total numbers of cDNA clones per sample are given in the bottom line. A number of sequences among the np9 cDNA sequences could not be assigned with certainty to specific HML-2 loci in the human reference genome or non-reference HML-2 sequences and were therefore categorized as “ambiguous”. Note that a number of cDNA sequences isolated from sample #35 and assignable to HML-2 type 2 locus chr3q21.2_K-4 appeared as alternatively spliced transcripts of an np9-typical length. The same was true for a cDNA sequence isolated from sample 5458-SC and assignable to locus chr3q21.2_K-4. See Table 1 for the three rightmost columns
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