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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