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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