FILTERS:
pvalue:0.1
Motif craMmus291005
More information about this gene at Ensembl.org Go to UCSC
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This page describes one atomic motif in this cisRED database. An atomic motif is a result returned by cisRED's motif discovery process operating on an input sequence set. An input sequence set consists of a search region sequence on the target genome (shown in the genome browser view below) and corresponding sequences from other species. A motif consists of a set of conserved sequences ('hits'). It can be represented by a consensus sequence, a position frequency matrix and a sequence logo.

Page Contents

Overview
Sequence Conservation
Motif overview
Atomic motif id craMmus291005
Discovery p-value 2.79E-03
Motif location chr2: 88,673,884-88,673,893 (+) (10 bp)
Search region location chr2: 88,673,281-88,675,034 (+) (1,754 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 11 species: Mus musculus, Canis familiaris, Dasypus novemcinctus, Danio rerio, Fugu rubripes, Homo sapiens, Loxodonta africana, Macaca mulatta, Rattus norvegicus, Sus scrofa, Spermophilus tridecemlineatus
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 5 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (5 annot.): AFP1(1.89E-04) ,    POU3F2(2.36E-04) ,    POU3F1(3.53E-04) ,    S8(8.95E-04) ,    SRY(9.34E-04)
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
43 (MEF-2A__POU3F2)     206 (AFP1__FOXD3)     340 (Cdx-2__POU3F2)     362 (OCA-B__POU3F2)     363 (IRF-1__POU3F1)     366 (HNF-3__POU3F1)     399 (POU3F2__aMEF-2)     402 (OCA-B__POU3F1)     412 (AFP1__IRF-1)     560 (FOXD3__POU3F1)     627 (AFP1__RSRFC4)     646 (POU2F1__POU3F1)     704 (AIRE__POU3F1)     728 (HNF-3alpha__POU3F2)     740 (AFP1__AIRE)     751 (AFP1__POU2F1)     762 (AFP1__aMEF-2)     792 (AFP1__OCA-B)     802 (POU3F1__aMEF-2)     805 (AFP1__MEF-2A)     858 (HNF-3__POU3F2)     919 (Nkx3-1__POU3F2)     944 (POU3F2__RSRFC4)     998 (POU2F1__POU3F2)     1007 (FOXD3__POU3F2)     1059 (AFP1__Nkx3-1)     1185 (AIRE__POU3F2)     1204 (AFP1__HNF-3)     1235 (MEF-2A__POU3F1)     1274 (Nkx3-1__POU3F1)     1467 (POU3F1__RSRFC4)     1520 (Cdx-2__POU3F1)     1547 (AFP1__Cdx-2)     1578 (IRF-1__POU3F2)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence AwAyAwTkAA TTmAsTrTsT
Position frequency matrix
1 2 3 4 5 6 7 8 9 10
A 11 6 11 0 9 7 3 0 11 11
C 0 0 0 4 0 0 0 0 0 0
G 0 0 0 0 0 0 0 5 0 0
T 0 5 0 7 2 4 8 6 0 0
A w A n A n T k A A
1 2 3 4 5 6 7 8 9 10
A 0 0 6 8 4 2 7 0 5 0
C 0 0 5 0 0 0 0 0 0 0
G 0 0 0 0 0 0 4 0 0 0
T 11 11 0 3 7 9 0 11 6 11
T T m A n T n T w T

In the table below, bases highlighted on the Target sequence will link to a single nucleotide polymoprhism in NCBI's dbSNP.

Site Sequence Stack
Ensembl gene ID Type Species Position Std (+)Sequence Std (-)Sequence
ENSMUSG00000057447 Target Mus musculus chr2:88,673,884-88,673,893 + ATACAATTAA – TTAATTGTAT
ENSMUSG00000057447_CFAM Orthologue Canis familiaris chr18:43,447,603-43,447,612 – AAATAATTAA + TTAATTATTT
ENSMUSG00000057447_DNOV Orthologue Dasypus novemcinctus scaffold_204744:1,050-1,059 – AAATTAAGAA + TTCTTAATTT
ENSMUSG00000057447_DRER Orthologue Danio rerio chr10:33,720,402-33,720,411 – AAACAATTAA + TTAATTGTTT
ENSMUSG00000057447_FRUB Orthologue Fugu rubripes chrUn:198,144,984-198,144,993 – ATACATAGAA + TTCTATGTAT
ENSMUSG00000057447_HSAP Orthologue Homo sapiens chr11:55,128,609-55,128,618 – ATATATTGAA + TTCAATATAT
ENSMUSG00000057447_LAFR Orthologue Loxodonta africana scaffold_41069:4,506-4,515 + ATATAATTAA – TTAATTATAT
ENSMUSG00000057447_MMUL Orthologue Macaca mulatta SCAFFOLD5079:98,264-98,273 – ATATATTTAA + TTAAATATAT
ENSMUSG00000057447_RNOR Orthologue Rattus norvegicus chr3:72,812,423-72,812,432 + AAATAAATAA – TTATTTATTT
ENSMUSG00000057447_SSCR Orthologue Sus scrofa ENSMUSG00000057447_SSCR:160-169 – AAACAATGAA + TTCATTGTTT
ENSMUSG00000057447_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000057447_STRI:47-56 – AAATTTTGAA + TTCAAAATTT

Questions or comments: cisred@bcgsc.ca