FILTERS:
pvalue:0.1
Motif craMmus342794
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 craMmus342794
Discovery p-value 2.79E-03
Motif location chr2: 87,700,803-87,700,810 (+) (8 bp)
Search region location chr2: 87,699,393-87,701,092 (+) (1,700 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 18 species: Mus musculus, Canis familiaris, Choloepus hoffmanni, Dasypus novemcinctus, Danio rerio, Felis catus, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Procavia capensis, Pan troglodytes, Rattus norvegicus, Sus scrofa, Tupaia belangeri, Xenopus tropicalis
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 8 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (6 annot.): POU3F2(1.32E-04) ,    Chx10(2.47E-04) ,    POU6F1_(c2)(2.85E-04) ,    HOXA5(3.00E-04) ,    Cdx-2(6.20E-04) ...
ORegAnno: (2 annot.): FoxA1(4.08E-04) ,    FoxA1(9.65E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
39 (Cdx-2__HOXA5)     43 (MEF-2A__POU3F2)     226 (POU3F2__S8)     250 (POU6F1_(c2)__RSRFC4)     252 (POU3F2__POU3F2)     254 (Cdx-2__Chx10)     265 (Chx10__MEF-2A)     285 (HNF-1alpha__POU6F1_(c2))     303 (Chx10__POU3F1)     317 (POU6F1_(c2)__aMEF-2)     339 (HOXA5__S8)     340 (Cdx-2__POU3F2)     358 (Chx10__POU2F1)     361 (HOXA5__POU3F2)     399 (POU3F2__aMEF-2)     435 (HOXA5__MEF-2A)     438 (HOXA5__POU2F1)     465 (HOXA5__RSRFC4)     536 (Chx10__HNF-1alpha)     682 (POU3F2__SRY)     707 (Chx10__S8)     725 (HOXA5__SRY)     755 (POU3F1__POU3F2)     942 (POU2F1__POU6F1_(c2))     944 (POU3F2__RSRFC4)     998 (POU2F1__POU3F2)     1062 (HNF-1alpha__HOXA5)     1089 (Chx10__SRY)     1177 (POU6F1_(c2)__S8)     1271 (MEF-2A__POU6F1_(c2))     1336 (POU3F2__POU6F1_(c2))     1410 (Cdx-2__POU6F1_(c2))     1429 (Chx10__RSRFC4)     1442 (Chx10__POU3F2)     1457 (POU3F1__POU6F1_(c2))     1464 (HOXA5__aMEF-2)     1471 (Chx10__aMEF-2)     1476 (HNF-1alpha__POU3F2)     1537 (POU6F1_(c2)__SRY)     1583 (HOXA5__POU3F1)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence AATGAATT AATTCATT
Position frequency matrix
1 2 3 4 5 6 7 8
A 18 15 2 2 18 13 0 0
C 0 3 0 0 0 0 0 0
G 0 0 0 16 0 0 0 0
T 0 0 16 0 0 5 18 18
A A T G A A T T
1 2 3 4 5 6 7 8
A 18 18 5 0 0 16 0 0
C 0 0 0 0 16 0 0 0
G 0 0 0 0 0 0 3 0
T 0 0 13 18 2 2 15 18
A A T T C A T 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
ENSMUSG00000047039 Target Mus musculus chr2:87,700,803-87,700,810 + AATAAATT – AATTTATT
ENSMUSG00000047039_CFAM Orthologue Canis familiaris chr18:43,080,544-43,080,551 + AATGAATT – AATTCATT
ENSMUSG00000047039_CHOF Orthologue Choloepus hoffmanni ENSMUSG00000047039_CHOF:212-219 + ACTGAATT – AATTCAGT
ENSMUSG00000047039_DNOV Orthologue Dasypus novemcinctus scaffold_18954:3,984-3,991 – AATGAATT + AATTCATT
ENSMUSG00000047039_DRER Orthologue Danio rerio chr10:33,665,427-33,665,434 + AATGATTT – AAATCATT
ENSMUSG00000047039_FCAT Orthologue Felis catus ENSMUSG00000047039_FCAT:130-137 + AATGAATT – AATTCATT
ENSMUSG00000047039_GGAL Orthologue Gallus gallus chr5:2,409,380-2,409,387 – AATGAATT + AATTCATT
ENSMUSG00000047039_HSAP Orthologue Homo sapiens chr11:55,438,666-55,438,673 – AATGATTT + AAATCATT
ENSMUSG00000047039_LAFR Orthologue Loxodonta africana scaffold_1215:49,017-49,024 + ACTGAATT – AATTCAGT
ENSMUSG00000047039_MDOM Orthologue Monodelphis domestica scaffold_33:16,677,844-16,677,851 + AATGAATT – AATTCATT
ENSMUSG00000047039_MMUL Orthologue Macaca mulatta SCAFFOLD115116:157,227-157,234 + AATGATTT – AAATCATT
ENSMUSG00000047039_OCUN Orthologue Oryctolagus cuniculus scaffold_108611:382-389 – AAAGAATT + AATTCTTT
ENSMUSG00000047039_PCAP Orthologue Procavia capensis ENSMUSG00000047039_PCAP:340-347 + ACTGAATT – AATTCAGT
ENSMUSG00000047039_PTRO Orthologue Pan troglodytes 9_random:27,081,488-27,081,495 – AATGATTT + AAATCATT
ENSMUSG00000047039_RNOR Orthologue Rattus norvegicus chr3:71,559,478-71,559,485 – AATAAATT + AATTTATT
ENSMUSG00000047039_SSCR Orthologue Sus scrofa ENSMUSG00000047039_SSCR:216-223 – AATGAATT + AATTCATT
ENSMUSG00000047039_TBEL Orthologue Tupaia belangeri ENSMUSG00000047039_TBEL:57-64 + AAAGAATT – AATTCTTT
ENSMUSG00000047039_XTRO Orthologue Xenopus tropicalis scaffold_10:4,059,795-4,059,802 + AATGATTT – AAATCATT

Questions or comments: cisred@bcgsc.ca