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Table 4 Transcription factor binding motifs in the upstream genome sequences of DE miRNA genes

From: Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection

miRNA gene

upstream TATA-box

ISRE-IRF1 M00972

IRF1 M00747

PU.1

GAS

IRF3 M00772

IRF8 M01665

NF-kappaB M00051

ETS2 M00340

Genbank Accesion #

miR462a/731 cluster

1

2

1

1

2

1

1

-

-

gi|925216714:63629639-63631038 (NC_027314.1)

ssa-mir-462b

1

2

1

1

1

2

1

-

-

gi|925216718:28307432-28308831 (NC_027312.1)

ssa-mir-146a-1

-

-

-

-

3

-

1

-

-

gi|925216706:4556929-4558189 (NC_027317.1)

ssa-mir-146a-2

-

-

-

-

2

-

-

-

-

gi|925216783:47301787-47303047 (NC_027300.1)

ssa-mir-146b

-

1

1

-

5

-

1

-

-

gi|925216704:2641623-2642883 (NC_027318.1)

ssa-mir-146a-3

-

-

3

-

3

-

-

-

-

gi|925216704:51691919-51693179 (NC_027318.1)

ssa-mir-21a-1

2

-

-

-

1

-

1

-

-

gi|925216727:116610294-116611574 (NC_027308.1)

ssa-mir-21a-2

1

-

-

-

1

-

2

-

-

gi|925216702:60966622-60967902 (NC_027319.1)

ssa-mir-21b-1

1

-

-

-

1

-

1

-

-

gi|925216769:50774080-50775360 (NC_027303.1)

ssa-mir-21b-2

-

-

1

-

1

1

1

-

-

gi|925216718:73813159-73814439 (NC_027312.1)

ssa-mir-1338

-

-

2

-

1

-

2

-

-

gi|925216772:45802741-45804012 (NC_027302.1)

ssa-mir-155-1

-

1

-

-

6

-

-

1

1

gi|925146043:6698-7958 (NW_012350889.1)

ssa-mir-92a-3

-

-

-

-

1

-

-

-

-

gi|925125935:50220-51479 (NW_012343521.1)

ssa-mir-7132b-1

2

-

-

1

4

-

-

-

-

gi|925216780:44866633-44867894 (NC_027301.1)

ssa-mir-7132b-2

3

-

-

1

1

-

-

-

-

gi|925216720:24179665-24180926 (NC_027311.1)

ssa-mir-7132a-1

-

-

1

1

1

-

1

-

-

gi|925216772:70457167-70458424 (NC_027302.1)

ssa-mir-7132a-2

-

-

1

1

1

-

-

-

-

gi|925216757:28942285-28943542 (NC_027305.1)

ssa-mir-734

-

-

-

-

-

-

-

-

-

gi|925216691:29709642-29710902 (NC_027324.1)

ssa-mir-181b

1

-

-

-

-

1

-

-

-

gi|925216772:43728947-43730207 (NC_027302.1)

ssa-mir-181c

1

-

-

-

2

-

-

-

-

gi|925216723:49524703-49525962 (NC_027310.1)

ssa-mir-2188-1

-

-

-

-

-

-

-

-

-

gi|925216702:26812353-26813612 (NC_027319.1)

ssa-mir-2188-2

-

-

-

-

-

-

-

-

-

gi|925216694:16936155-16937414 (NC_027323.1)

miR-223-1

1

-

1

-

4

-

1

-

-

gi|925216769:43698893-43700211 (NC_027303)

miR-223-2

-

-

1

-

2

1

1

-

-

gi|925216718:81008935-81010247 (NC_027312.1)

  1. Consensus sequences to each of the nine cis-elements are given in Additional file 4
  2. Genbank accession # gives the complete genome sequences spanning the miRNA genes analysed
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BMC Genomics

ISSN: 1471-2164

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