FILTERS:
pvalue:0.1
Motif craMmus168473
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 craMmus168473
Discovery p-value 2.79E-03
Motif location chr2: 87,711,291-87,711,298 (+) (8 bp)
Search region location chr2: 87,710,132-87,711,908 (+) (1,777 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 16 species: Mus musculus, Canis familiaris, Dasypus novemcinctus, Danio rerio, Echinops telfairi, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macropus eugenii, Macaca mulatta, Oryctolagus cuniculus, Procavia capensis, Pan troglodytes, Rattus norvegicus, Xenopus tropicalis
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 6 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (5 annot.): POU3F2(5.11E-05) ,    POU6F1_(c2)(1.25E-04) ,    Chx10(1.40E-04) ,    IPF1(4.62E-04) ,    Lhx3a(5.52E-04)
ORegAnno: (1 annot.): FoxA1(6.44E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
38 (Nkx6-2__POU6F1_(c2))     79 (Nkx6-2__POU3F2)     160 (POU1F1__POU3F2)     167 (FOXP1a__POU6F1_(c2))     282 (FOXP1a__POU3F2)     285 (HNF-1alpha__POU6F1_(c2))     317 (POU6F1_(c2)__aMEF-2)     338 (Chx10__IPF1)     361 (HOXA5__POU3F2)     384 (Chx10__FOXJ2)     399 (POU3F2__aMEF-2)     417 (POU6F1_(c2)__POU6F1_(c2))     498 (Chx10__HOXA5)     536 (Chx10__HNF-1alpha)     611 (Chx10__POU1F1)     636 (IPF1__POU3F2)     709 (IPF1__POU6F1_(c2))     914 (Chx10__POU6F1_(c2))     1016 (FOXJ2__POU6F1_(c2))     1064 (Chx10__FOXP1a)     1069 (POU1F1__POU6F1_(c2))     1233 (FOXJ2__POU3F2)     1336 (POU3F2__POU6F1_(c2))     1373 (HOXA3__POU3F2)     1441 (HOXA5__POU6F1_(c2))     1471 (Chx10__aMEF-2)     1476 (HNF-1alpha__POU3F2)     1559 (Chx10__Nkx6-2)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence wTmATTTA TAAATkAs
Position frequency matrix
1 2 3 4 5 6 7 8
A 9 0 10 16 2 0 0 16
C 1 0 6 0 0 0 0 0
G 0 0 0 0 0 0 0 0
T 6 16 0 0 14 16 16 0
w T n A T T T A
1 2 3 4 5 6 7 8
A 0 16 16 14 0 0 16 6
C 0 0 0 0 0 0 0 0
G 0 0 0 0 0 6 0 1
T 16 0 0 2 16 10 0 9
T A A A T n A 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
ENSMUSG00000045225 Target Mus musculus chr2:87,711,291-87,711,298 + TTAATTTA – TAAATTAA
ENSMUSG00000045225_CFAM Orthologue Canis familiaris chr18:43,090,961-43,090,968 – TTAATTTA + TAAATTAA
ENSMUSG00000045225_DNOV Orthologue Dasypus novemcinctus scaffold_8444:2,813-2,820 – TTAATTTA + TAAATTAA
ENSMUSG00000045225_DRER Orthologue Danio rerio chr10:33,688,433-33,688,440 – ATAATTTA + TAAATTAT
ENSMUSG00000045225_ETEL Orthologue Echinops telfairi scaffold_184773:952-959 + ATAATTTA – TAAATTAT
ENSMUSG00000045225_GGAL Orthologue Gallus gallus chr5:72,966-72,973 – TTAATTTA + TAAATTAA
ENSMUSG00000045225_HSAP Orthologue Homo sapiens chr11:55,438,755-55,438,762 – ATAATTTA + TAAATTAT
ENSMUSG00000045225_LAFR Orthologue Loxodonta africana scaffold_1215:66,985-66,992 + ATCAATTA – TAATTGAT
ENSMUSG00000045225_MDOM Orthologue Monodelphis domestica scaffold_33:16,664,175-16,664,182 – ATCATTTA + TAAATGAT
ENSMUSG00000045225_MEUG Orthologue Macropus eugenii ENSMUSG00000045225_MEUG:687-694 + ATCATTTA – TAAATGAT
ENSMUSG00000045225_MMUL Orthologue Macaca mulatta SCAFFOLD115116:157,141-157,148 + ATAATTTA – TAAATTAT
ENSMUSG00000045225_OCUN Orthologue Oryctolagus cuniculus scaffold_173414:66,399-66,406 – TTCATTTA + TAAATGAA
ENSMUSG00000045225_PCAP Orthologue Procavia capensis ENSMUSG00000045225_PCAP:72-79 + CTAATTTA – TAAATTAG
ENSMUSG00000045225_PTRO Orthologue Pan troglodytes 9_random:27,081,578-27,081,585 – ATAATTTA + TAAATTAT
ENSMUSG00000045225_RNOR Orthologue Rattus norvegicus chr3:71,570,929-71,570,936 + ATCATTTA – TAAATGAT
ENSMUSG00000045225_XTRO Orthologue Xenopus tropicalis scaffold_10:4,090,849-4,090,856 + TTCAATTA – TAATTGAA

Questions or comments: cisred@bcgsc.ca