FILTERS:
pvalue:0.1
Motif craMmus417460
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 craMmus417460
Discovery p-value 2.79E-03
Motif location chr2: 87,374,571-87,374,580 (+) (10 bp)
Search region location chr2: 87,374,174-87,375,950 (+) (1,777 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 13 species: Mus musculus, Canis familiaris, Cavia porcellus, Dasypus novemcinctus, Danio rerio, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Pan troglodytes, Rattus norvegicus
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 2 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (2 annot.): POU3F2(1.08E-04) ,    POU1F1(3.81E-04)
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
43 (MEF-2A__POU3F2)     53 (POU1F1__aMEF-2)     79 (Nkx6-2__POU3F2)     85 (OCA-B__POU1F1)     145 (COMP1__POU3F2)     147 (AFP1__POU3F2)     160 (POU1F1__POU3F2)     175 (HMG_I__POU3F2)     176 (C-EBPgamma__POU1F1)     252 (POU3F2__POU3F2)     340 (Cdx-2__POU3F2)     361 (HOXA5__POU3F2)     362 (OCA-B__POU3F2)     399 (POU3F2__aMEF-2)     456 (POU1F1__YY1)     476 (E4BP4__POU3F2)     477 (HOXA5__POU1F1)     497 (E4BP4__POU1F1)     522 (POU1F1__POU2F1)     562 (POU3F2__YY1)     606 (COMP1__POU1F1)     636 (IPF1__POU3F2)     657 (FOXD3__POU1F1)     998 (POU2F1__POU3F2)     1007 (FOXD3__POU3F2)     1044 (Cdx-2__POU1F1)     1084 (POU1F1__Pax-6)     1104 (Nkx6-2__POU1F1)     1153 (C-EBPgamma__POU3F2)     1156 (POU3F2__Pax-6)     1167 (POU3F2__TEF)     1196 (POU1F1__TEF)     1362 (HMG_I__POU1F1)     1476 (HNF-1alpha__POU3F2)     1517 (AFP1__POU1F1)     1574 (IPF1__POU1F1)     1584 (MEF-2A__POU1F1)     1600 (HNF-1alpha__POU1F1)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence wwTACATGTA TACATGTAss
Position frequency matrix
1 2 3 4 5 6 7 8 9 10
A 6 5 0 13 0 12 0 4 0 13
C 0 0 2 0 11 0 0 0 0 0
G 0 0 0 0 0 0 4 9 0 0
T 7 8 11 0 2 1 9 0 13 0
w n T A C A T G T A
1 2 3 4 5 6 7 8 9 10
A 0 13 0 9 1 2 0 11 8 7
C 0 0 9 4 0 0 0 0 0 0
G 0 0 0 0 0 11 0 2 0 0
T 13 0 4 0 12 0 13 0 5 6
T A C A T G T A n w

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
ENSMUSG00000061520 Target Mus musculus chr2:87,374,571-87,374,580 + TATACATGTA – TACATGTATA
ENSMUSG00000061520_CFAM Orthologue Canis familiaris chr18:43,070,803-43,070,812 + TTTACAGATA – TATCTGTAAA
ENSMUSG00000061520_CPOR Orthologue Cavia porcellus ENSMUSG00000061520_CPOR:531-540 + ATTACTGATA – TATCAGTAAT
ENSMUSG00000061520_DNOV Orthologue Dasypus novemcinctus scaffold_18954:3,528-3,537 – TTTACAGATA + TATCTGTAAA
ENSMUSG00000061520_DRER Orthologue Danio rerio chr21:14,235,032-14,235,041 – AATACATGTA + TACATGTATT
ENSMUSG00000061520_GGAL Orthologue Gallus gallus chr5:71,185-71,194 + TTTACATGTA – TACATGTAAA
ENSMUSG00000061520_HSAP Orthologue Homo sapiens chr11:55,439,124-55,439,133 + ATTACATGTA – TACATGTAAT
ENSMUSG00000061520_LAFR Orthologue Loxodonta africana scaffold_13558:5,585-5,594 + TTCACATGTA – TACATGTGAA
ENSMUSG00000061520_MDOM Orthologue Monodelphis domestica scaffold_33:17,365,646-17,365,655 – TATACAGATA + TATCTGTATA
ENSMUSG00000061520_MMUL Orthologue Macaca mulatta SCAFFOLD115116:156,233-156,242 – ATCACATGTA + TACATGTGAT
ENSMUSG00000061520_OCUN Orthologue Oryctolagus cuniculus scaffold_170859:3,081-3,090 – AATATATGTA + TACATATATT
ENSMUSG00000061520_PTRO Orthologue Pan troglodytes 9_random:27,081,944-27,081,953 + ATTACATGTA – TACATGTAAT
ENSMUSG00000061520_RNOR Orthologue Rattus norvegicus chr3:71,098,846-71,098,855 + TATATATGTA – TACATATATA

Questions or comments: cisred@bcgsc.ca