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Table 2 Primers used for assay design.

From: A systematic evaluation of expression of HERV-W elements; influence of genomic context, viral structure and orientation

Target

LTR status

Polarity

Sequence

Position

Target

Polarity

Sequence

Position

Intronic HERV-W proviral element (3' region)

 

Gene harboring provirus

Sense

        

CD72 intron 1

3'

F

TGTCTCCAATTTTAACCCTATTTGC

chr9:35629741

CD72 exon 1~2

F

CTCTAGCTGATCGACTCACAAATACC

AK311283

  

R

TTCCCCAGCCAGCATGTAA

chr9:35629792

 

R

TGAACATTCTCGTAGGTGATTTCC

 

TBX18 intron 7

5'&3'

F

CCATTCCATGTTCCTCATTAAATCT

chr6:85477157

TBX18 exon 7~8

F

CCCAAGCAAGAATACAGGGACTT

BC040697

  

R

AGGCAATCTTACCACCCAGAAG

chr6:85477208

 

R

GGTTTCCCTTGAGACCAAATTG

 

Antisense

        

ACOX3 intron 1

5'&3'

F

AGACGCTTGGAGCAGTTTCTG

chr4:8480630

ACOX3 exon 1~2

F

CTGTGGAGTGTGTGGGCTCTT

AK225080

  

R

TCGGAGGACTTTACACATTGAACTAG

chr4:8480744

 

R

CAGAGCTGTGTCGCCTCCTT

 

KYNU intron 2

5'&3'

F

AGTGGGAATACTGACGCTCTTACC

chr2:143372701

KYNU exon 2~3

F

ACAGGATCTGCCTCCAGTTGA

U57721

  

R

GCCAAGAACCCAAGGTCAGA

chr2:143372792

 

R

TGGCCCACTTATCTAGTTCTTCTTC

 

THEM2 intron 1

5'

F

TGAGATACCAGAGATCACCAAACTCTT

chr6:24787905

THEM2 exon 1~2

F

GGGAGGTGATAAAGGCCATGA

BC000894

  

R

TGAAGTTTTATAAGGGTTAGGACAATCTT

chr6:24788017

 

R

GGAGCAGCAGAGACAAGAGTAATCT

 

ZNF678 intron 1

5'&3'

F

GGAAATGAACATAGTCTTACTGTCAGGTA

chr1:225878139

ZNF678 exon 1~2

F

TGCAGGTACTGGGAGTTACATAGC

BC042500

  

R

CATAGAGTCCAGAAATGTGTCTATCCA

chr1:225878254

 

R

TGCCAGTAGTCCCGTTTTCC

 

ANO3 intron 14

3'

F

AAAGGATTGTGTAAGAGAAGCTGATAAGA

chr11:26568090

ANO3 exon 14~15

F

TTGTTCGATAATGGAGGGACAGT

BC172396

  

R

GCAGAGATGTTATCCCTGTTGGT

chr11:26568167

 

R

CGATAAGGTCCCAAGTATAGGTCAGT

 

Intronic HERV-W proviral element (5' region)

CD72 intron 1

 

F

GCAGAGGTCTACTCACACCATAGC

chr9:35633414

    
  

R

GGCAATCAGGAGGCCTAAA

chr9:35633462

    

TBX18 intron 7

 

F

GGGCTACAGTGATCCATTTATAAGG

chr6:85488459

    
  

R

AAACTTTATCCAAACATTCCCTATGTTAG

chr6:85488532

    

ANO3 intron 14

 

F

TCTCCTTCACCACGAGAGTTTG

chr11:26576040

    
  

R

TGCTACTCGTCCAGAGCTTACAGA

chr11:26576091

    

Intronic HERV-W pseudoelement (3' region)

 

Gene harboring pseudoelement

Sense

        

SLC16A10 intron 1

 

F

TGGCAGTGCTCGTTGAATGT

chr6:111566680

SLC16A10 exon 1~2

F

GGCTCCAAAGACGATGACAAG

BC034031

  

R

ACATAAGCCCCAAAACTGTCAGA

chr6:111566728

 

R

AAATCATCCCCATGGAGAGAGA

 

AK024261 intron 1

 

F

GGCCCACCTCCAGCAAA

chr2:218160716

AK024261 exon 1~2

F

CAGCAGATGATGGTGATGGAA

AK024261

  

R

TGGGTGTGATCAGGTCATGGT

chr2:218160778

 

R

CATCCCTCGGACTCAGTTTCTC

 

Antisense

        

FOXP2 intron 3

 

F

CAAGAGGACATCTCTAAATCAAAGACTGT

chr7:113805180

FOXP2 exon 3~4

F

GCGAGGTTAATTCGAAAGTCTTGTGGAA

AF454830

  

R

GAGCATGCCAGGCAAAGC

chr7:113805235

 

R

TTGCTTATTGTCTCTGTCGCAGAT

 

APG5 intron 6

 

F

TCAAATCACACAATGCTCCAATG

chr6:106791850

APG5 exon 6~7

F

ATCCCCTTTAGAATATATCAGACAACGA

BC093011

  

R

TTAGCAGTTGCATATGAGATCTTTCA

chr6:106791905

 

R

CCTAGTGTGTGCAACTGTCCATCT

 

KIAA0423 intron7

 

F

GACATGAATATTTTTTGTGGACATAACTC

chr14:44557550

KIAA0423 exon 7~8

F

CCAACAAGACTTTCTTCTGCAAAG

AB007883

  

R

GCCAAACAGAACAGTACTAAACTATATTATAGACT

chr14:44557636

 

R

TTTGCTGTGGATTTGATGATGAC

 

NRCAM intron 2

 

F

AAGTCTGGGTTCCAGGTTCATC

chr7:107772873

NRCAM exon 2~3

F

GCTGGTCTTAGCTGTTGGCATT

BC115736

  

R

CTGAGGAACCTTTCTGAGTTGAGTAA

chr7:107772929

 

R

CGTCTTCTTAGCATTGCTCTTCAG

 

ZMAT3 intron 2

 

F

GGATTCCCAGGTACGGTGAAA

chr3:180258291

ZMAT3 exon 2~3

F

CTCTGCAATGTCACCTTGAACTCT

BC002896

  

R

CCTAGAAAGCTACTTCCGCTTCAG

chr3:180258381

 

R

GCTGCATAGTAATTTCGGAGTTTCT

 

Intronic HERV-W pseudoelement (5' region)

SLC16A10 intron 1

 

F

CAAGAGGACATCTCTAAATCAAAGACTGT

chr6:111558508

    
  

R

GAGCATGCCAGGCAAAGC

chr6:111558555

    

FOXP2 intron 3

 

F

TCAAATCACACAATGCTCCAATG

chr7:113813845

    
  

R

TTAGCAGTTGCATATGAGATCTTTCA

chr7:113813901

    

NRCAM intron 2

 

F

GACATGAATATTTTTTGTGGACATAACTC

chr7:107763923

    
  

R

GCCAAACAGAACAGTACTAAACTATATTATAGACT

chr7:107763973

    

Intronic solitary LTR

 

Gene harboring solitary LTR

Sense

        

ZNF 277 intron 1

 

F

AGAACCCAGGTCAGAAAACAAGAG

chr7:111648615

ZNF277 exon 1~2

F

GGCTGTCGCCCGAATG

AF209198

  

R

CAGTCCCTGGTGCCAAGAAG

chr7:111648735

 

R

ACAATCCTTACTGTCCCCATAACC

 

WDR72 intron 14

 

F

AAACACTATCTGATTGCCTGACAGA

chr15:51704774

WDR72 exon 14~15

F

CCAGCTTGGGCCATTACCTT

BX53788

  

R

CCAGGACCTTGTCTATGATGCA

chr15:51704828

 

R

GCAAAATTTGGCATCAGTAACCT

 

chrXq13.1

 

F

CAGGTCCATTTAAAGCCCAAGT

chrX:71350691

PIN4 exon 3~4

F

CAGGTCCATTTAAAGCCCAAGT

AK12760

  

R

CCTGAAAGTGAAGCCAAAAGGA

chrX:71350741

 

R

CCTGAAAGTGAAGCCAAAAGGA

 

chrXq26.2

 

F

TGGGAGAAGCAATGTCCAATT

chrX:131380909

MBNL3 exon 1~2

F

TGGCCTGTTTTGATTCTCTAAAGG

AB077698

  

R

TTTGTCAAGTCATGGCCGTTT

chrX:131380961

 

R

AGTGTGGAGGAGGGTGAAGGT

 

Antisense

        

C9orf85 intron 2

 

F

ACCCACCAATTCCGGATACA

chr9:73769452

C9orf85 exon 2~3

F

GAGTGGCGTGTAAAATACAGCAAA

BC052375

  

R

TGGCCCAAGATTTCATTCCT

chr9:73769523

 

R

CATGGCCTGCACATTATGTGA

 
     

UBD exon 1~2

F

GATGGCTCCCAATGCTTCCT

AF123050

      

R

TGGCATCAAAGGTCATTAAATCC

 

chr6p22.1

 

F

GCCAGATAACCAGCTTCTCTTCA

chr6:29635237

GABBR1 exon 18~19

F

GGAGTCGAGTGCATTTGCTTTAT

BC051463

  

R

GAGAAGAGGCTGGCATTGACA

chr6:29635286

 

R

TGGCATCAAAGGTCATTAAATCC

 

chrXq13.1

    

ERCC6L exon 1~2

F

GGAAGCCGAGGCCTTGAG

BC111486

      

R

TTAGTTGCTTCTTTGGCCTCTTTC

 

chrXq26.2

    

AK095439 exon 2~3

F

ACTTCATTGAATGTCTTAGACGGAAA

AK09543

      

R

TCACATATGCAGTTATCAAAAGAGCTT

 

Intergenic HERV-W proviral element and adjacent genes

 

Intergenic HERV-W pseudoelement and adjacent genes

LRIG3 (5')

 

F

TCGAGTAATTCTTTCATGGGTACCT

AY505340

COBLL1 (5')

F

CAGAGTTTGCTGACTGCAATCC

BC071588

  

R

ATCTGATGGCTGTCCAAAGCTT

  

R

GACCTTCCATTCACAGATATTGTATTTG

 

pro chr12q14,1

 

F

TGGTCAAGAGGAGTCCAGAGTTT

chr12:57530852

pse chr2q24,3

F

ACCTACACCAATTCAGCTGTTAAGG

chr2:165222305

  

R

GCCCACCAATGCAATGCT

chr12:57530902

 

R

CCACAATGCTCCGAGTTCACT

chr2:165222360

AK093124 (3')

 

F

TGTCCCTTGCTACATACCTGCTT

 

GRB14 (3')

F

TGTGCTGCAGACAGGCGAAAA

 
  

R

TGCACTCAGATAAAGTGTCAATAAGAAG

AK093124

 

R

CAGATGTAAATGGAGAACAGCATAGC

BC053559

GSTA4

  

N/A

 

GRK7 (5')

F

TGCAGGCTCTTCTTGGCTAAG

AF439409

      

R

GTTTCCTGGGATCATCAGAATTTT

 

pro chr6p12,1

 

F

GACCTTTTTCCTGGGCATCA

chr6:52887125

pse chr3q23

F

GGGTCCAAGGCTGCTCCTA

chr3:143023903

  

R

GGGTAGGTGAACATGCCAGAA

chr6:52887169

 

R

GGTAAGCCTCCTGCACTCTGA

chr3:143023960

GSTA3 (3')

 

F

GCGGAGACCGGCTAGACTTT

 

ATP1B3

 

N/A

 
  

R

CCGTCCATTGAAGTAGTGAAGCT

BC020619

    

AKR1B10 (5')

 

F

TGCTGAGGAGATGGCAACCAT

B C008837

CLSTN3 (5')

F

GGGATGACTCAGCTCTCACCAT

BC039075

  

R

TCCAAATGAGAGGATTGCAACAC

  

R

TCACACAGGACTGCCGATTC

 

pro chr7q33

 

F

TGGAAGAAACAAATTGCCTGATC

chr7:133929406

pse chr12p13.31

F

CAGAAAGGTTTTGCCTAGTAGTGTTG

chr12:7230506

  

R

AAATGCCCTTAGGCCAGATAGAT

chr7:133929455

 

R

TGTGCTGTACTTCTGCTTTTTAGAAAT

chr12:7230605

BPGM (3')

 

F

GGTGGCCCCTTTGCAGAT

 

PEX5 (3')

F

ATGCAGCAGATTGAGCAGTCA

 
  

R

TGGACATACTGATGGCTGAACTTC

BC01705

 

R

CAGTTCTCAGACAAGGCCAAGTC

AK301700

TMEM26 (5')

 

F

TGCCATCCTTGTTATATGGACTTG

CR749606

INTS7 (5')

F

CACTGCAGAGTAAATCTGGACAAGA

BC020523

  

R

CAGGGCACACAACGTTCTGT

  

R

TCAACCCTTTGCTCCATCTCA

 

pro chr10q21.2

 

F

TGAAACGTGTCATGTATCATCTCAA

chr10:62462501

pse chr1q32.3

F

TCTGATGAACTCTGAATAAACTCTTTCT

chr1:210095554

  

R

GGTAACACCCGGCCATTTT

chr10:62462549

 

R

G

chr1:210095648

RHOBTB1 (3')

 

F

CCGCGGGAGCTTCCA

 

LPGAT1 (3')

F

GATTGCATGCCCTAATTATGGAA

 
  

R

CCATTTTCATAACTTAGTCAAGAATGCT

BC093035

 

R

CCCTGAGAGATCACCGAGAAAG

BC034621

LRRK2 (5')

 

F

GGTACACAAAAGCAGAAAGAGATACAA

chr7:133929455

RNGTT (5')

F

GCCACGGAGCTTCTTCCA

BC019954

  

R

TTTGCACTTCATGTGGAAGATTG

  

R

CAAAAGTTTTCCTAATGCCTACAACA

 

pro chr12q12

 

F

GGGAGCAGATGAGGAGCAAA

chr12:39072588

pse chr6q15

F

CATCTCCTTGGTGACAGGGTTT

chr6:89180050

  

R

GGTGGACCTGGAAAATGGAA

chr12:39072637

 

R

TGGTCACTTGATTTATAAGAAACGTGTT

chr6:89180152

CR749517 (3')

 

F

TTTGACTTACTCGTTCACTGTGATCA

 

CNR1 (3')

F

CCACATAGGACTGGTTTTCAATTG

 
  

R

TGTGGCTGCTGTGCTGAAA

CR749517

 

R

ATGCCTCCACCAGTGATTGC

AK313908

       

GGCCATCTAGGATCGACTTCAT

 
  1. Target, primer sequences and position of sequences used for assay design. The same orientation of HERV-W element or solitary LTR and genes harboring such elements is indicated by sense, whereas opposite orientation is indicated by anti-sense. For simplicity, intergenic HERV-W elements transcribed in the same orientation as their adjacent genes were selected. Genes located upstream and downstream of intergenic elements are labeled 5' and 3', respectively.