Transcriptome-wide microRNA target prediction including lncRNAs
miRcode 11 (June 2012) based on: UCSC GRCh37/hg19, GENCODE 11 transcripts, Multiz 46 species, TargetScan6 families
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Introduction

MiRcode provides "whole transcriptome" human microRNA target predictions based on the comprehensive GENCODE gene annotation, including >10,000 long non-coding RNA genes. Coding genes are also covered, including atypical regions such as 5'UTRs and CDS. MicroRNA family definitions and names are consistent with TargetScan. Site conservation is evaluated based on 46 vertebrates species. Data sources and stats is found on the data info page, and the FAQ answers many questions. Please cite the miRcode paper if this resource is useful in your research.

Do an interactive search below, browse sites in the UCSC browser, or download for local use.

Note that miRcode sites are now directly available through the UCSC browser Track Data Hubs feature.

Target site search

Gene (symbol/accession): MicroRNA family: (Highly conserved families)
Gene class: Any
LncRNA (all)
LncRNA (intergenic)
LncRNA (coding overlap)
Coding
Pseudogene
Other
 Site conservation: Any
Most primates
+Most mammals
+Most non-mammal vertebrates
 Transcript region: Any/ncRNA
3'UTR
CDS
5'UTR



Search result

ENSG00000228630.1 (HOTAIR) (lncRNA, overlapping)
microRNA familySeed positionSeed typeTranscript regionRepeatConservation
PrimatesMammalsOther vert.
miR-130ac/301ab/301b/301b-3p/454/721/4295/3666 chr12:54356628 7-mer-m8 ncRNA no 56 % 0 % 0 %
miR-133abc chr12:54357186 7-mer-m8 ncRNA no 22 % 0 % 0 %
miR-9/9ab chr12:54359834 7-mer-A1 ncRNA no 78 % 35 % 0 %
miR-138/138ab chr12:54358027 7-mer-A1 ncRNA no 78 % 96 % 0 %
miR-143/1721/4770 chr12:54357470 7-mer-m8 ncRNA no 89 % 61 % 0 %
miR-146ac/146b-5p chr12:54368731 8-mer ncRNA no 33 % 0 % 0 %
miR-148ab-3p/152 chr12:54356219 7-mer-m8 ncRNA no 78 % 22 % 0 %
miR-148ab-3p/152 chr12:54357267 7-mer-m8 ncRNA no 67 % 17 % 0 %
miR-148ab-3p/152 chr12:54361156 7-mer-A1 ncRNA no 78 % 9 % 0 %
miR-150/5127 chr12:54357123 7-mer-m8 ncRNA no 56 % 13 % 0 %
miR-17/17-5p/20ab/20b-5p/93/106ab/427/518a-3p/519d chr12:54356298 7-mer-m8 ncRNA no 67 % 35 % 0 %
miR-193/193b/193a-3p chr12:54357887 7-mer-A1 ncRNA no 22 % 4 % 0 %
miR-194 chr12:54356811 8-mer ncRNA no 78 % 22 % 0 %
miR-19ab chr12:54356629 7-mer-m8 ncRNA no 56 % 0 % 0 %
miR-1ab/206/613 chr12:54356155 7-mer-m8 ncRNA no 89 % 9 % 0 %
miR-203 chr12:54356379 7-mer-A1 ncRNA no 44 % 0 % 0 %
miR-204/204b/211 chr12:54357662 8-mer ncRNA no 89 % 26 % 0 %
miR-208ab/208ab-3p chr12:54356412 7-mer-A1 ncRNA no 44 % 0 % 0 %
miR-21/590-5p chr12:54357906 7-mer-m8 ncRNA no 56 % 70 % 8 %
miR-214/761/3619-5p chr12:54356646 7-mer-m8 ncRNA no 56 % 30 % 0 %
miR-216a chr12:54356471 7-mer-A1 ncRNA no 67 % 0 % 0 %
miR-216b/216b-5p chr12:54356471 7-mer-A1 ncRNA no 67 % 9 % 0 %
miR-217 chr12:54356266 7-mer-m8 ncRNA no 89 % 17 % 0 %
miR-217 chr12:54356591 7-mer-A1 ncRNA no 33 % 4 % 0 %
miR-217 chr12:54356658 7-mer-m8 ncRNA no 89 % 26 % 0 %
miR-217 chr12:54360112 7-mer-A1 ncRNA no 78 % 26 % 0 %
miR-221/222/222ab/1928 chr12:54356181 7-mer-m8 ncRNA no 89 % 35 % 0 %
miR-30abcdef/30abe-5p/384-5p chr12:54359820 8-mer ncRNA no 89 % 65 % 8 %
miR-103a/107/107ab chr12:54356645 7-mer-A1 ncRNA no 56 % 30 % 0 %
miR-103a/107/107ab chr12:54358040 7-mer-A1 ncRNA no 78 % 43 % 0 %
miR-124/124ab/506 chr12:54356205 7-mer-A1 ncRNA no 67 % 0 % 0 %
miR-33ab/33-5p chr12:54356385 7-mer-A1 ncRNA no 56 % 0 % 0 %
miR-34ac/34bc-5p/449abc/449c-5p chr12:54357537 7-mer-m8 ncRNA no 33 % 4 % 0 %
miR-375 chr12:54357754 7-mer-A1 ncRNA no 100 % 35 % 0 %
miR-10abc/10a-5p chr12:54368706 7-mer-m8 ncRNA no 67 % 9 % 0 %
miR-129-5p/129ab-5p chr12:54362588 7-mer-A1 ncRNA no 56 % 0 % 0 %
miR-129-5p/129ab-5p chr12:54362618 7-mer-m8 ncRNA no 56 % 0 % 0 %
miR-499-5p chr12:54356412 7-mer-A1 ncRNA no 44 % 0 % 0 %
ENSG00000233429.4 (HOTAIRM1) (other)
microRNA familySeed positionSeed typeTranscript regionRepeatConservation
PrimatesMammalsOther vert.
miR-135ab/135a-5p chr7:27138803 7-mer-A1 ncRNA no 67 % 0 % 0 %
miR-137/137ab chr7:27138561 8-mer ncRNA no 78 % 78 % 38 %
miR-148ab-3p/152 chr7:27139717 8-mer ncRNA no 56 % 0 % 0 %
miR-150/5127 chr7:27139432 7-mer-A1 ncRNA no 78 % 74 % 15 %
miR-17/17-5p/20ab/20b-5p/93/106ab/427/518a-3p/519d chr7:27139618 8-mer ncRNA no 67 % 70 % 15 %
miR-216a chr7:27138835 7-mer-m8 ncRNA no 11 % 0 % 0 %
miR-216a chr7:27139435 7-mer-A1 ncRNA no 78 % 26 % 0 %
miR-216b/216b-5p chr7:27139435 7-mer-A1 ncRNA no 78 % 26 % 0 %
miR-22/22-3p chr7:27135831 7-mer-m8 ncRNA no 56 % 4 % 0 %
miR-122/122a/1352 chr7:27138817 7-mer-m8 ncRNA no 56 % 0 % 0 %
miR-103a/107/107ab chr7:27138975 7-mer-m8 ncRNA no 67 % 22 % 0 %
miR-338/338-3p chr7:27135867 7-mer-A1 ncRNA no 33 % 0 % 0 %
miR-129-5p/129ab-5p chr7:27139762 8-mer ncRNA yes 56 % 0 % 0 %
miR-490-3p chr7:27135280 7-mer-m8 ncRNA no 56 % 61 % 23 %
miR-490-3p chr7:27138933 7-mer-m8 ncRNA no 56 % 0 % 0 %

53 matching sites.
Inquiries can be addressed to erik.larsson@gu.se