Skip to main content

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