cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000047039 > craMmus342950

Motif craMmus342950

More information about this gene at Ensembl.org

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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	craMmus342950
Discovery p-value	2.79E-03
Motif location	chr2: 87,700,857-87,700,866 (+) (10 bp)
Search region location	chr2: 87,699,393-87,701,092 (+) (1,700 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	17 species: Mus musculus, Bos taurus, Canis familiaris, Choloepus hoffmanni, Dasypus novemcinctus, Danio rerio, Erinaceus europaeus, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Pan troglodytes, Rattus norvegicus, Tupaia belangeri, Xenopus tropicalis
Found with	MotifSampler
'De Novo' motif group ID	This motif was not submitted for clustering.
Similar to (annotation p-value)	There are 4 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (4 annot.): MEF-2A(7.02E-05) , aMEF-2(7.62E-05) , HMG_I(6.00E-04) , Lmo2(9.70E-04) ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 43 (MEF-2A__POU3F2) 198 (HNF-1alpha__MEF-2A) 265 (Chx10__MEF-2A) 292 (Cdx-2__aMEF-2) 317 (POU6F1_(c2)__aMEF-2) 399 (POU3F2__aMEF-2) 435 (HOXA5__MEF-2A) 767 (HNF-1alpha__aMEF-2) 802 (POU3F1__aMEF-2) 851 (POU2F1__aMEF-2) 871 (MEF-2A__POU2F1) 934 (RSRFC4__aMEF-2) 936 (MEF-2A__RSRFC4) 978 (MEF-2A__YY1) 1055 (SRY__aMEF-2) 1160 (YY1__aMEF-2) 1231 (Cdx-2__MEF-2A) 1235 (MEF-2A__POU3F1) 1271 (MEF-2A__POU6F1_(c2)) 1450 (S8__aMEF-2) 1462 (MEF-2A__SRY) 1464 (HOXA5__aMEF-2) 1471 (Chx10__aMEF-2) 1601 (MEF-2A__S8) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

AAATAwCAwT

AsTGsTATTT

Position frequency matrix

	1	2	3	4	5	6	7	8	9	10
A	17	16	17	0	15	8	0	17	7	0
C	0	1	0	0	0	0	10	0	0	0
G	0	0	0	5	0	0	5	0	0	0
T	0	0	0	12	2	9	2	0	10	17
	A	A	A	T	A	w	s	A	w	T

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8	9	10
A	17	10	0	2	9	2	12	0	0	0
C	0	0	0	5	0	0	5	0	0	0
G	0	0	0	10	0	0	0	0	1	0
T	0	7	17	0	8	15	0	17	16	17
	A	w	T	s	w	T	A	T	T	T

Transfac

Jaspar

CSV

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

Ensembl gene ID	Type	Species	Position	Std	(+)Sequence	Std	(-)Sequence
Site Sequence Stack
ENSMUSG00000047039	Target	Mus musculus	chr2:87,700,857-87,700,866	+	AAATATCATT	–	AATGATATTT
ENSMUSG00000047039_BTAU	Orthologue	Bos taurus	chr1:22,333,776-22,333,785	+	AAATTAGAAT	–	ATTCTAATTT
ENSMUSG00000047039_CFAM	Orthologue	Canis familiaris	chr18:43,079,022-43,079,031	+	AAAGATCATT	–	AATGATCTTT
ENSMUSG00000047039_CHOF	Orthologue	Choloepus hoffmanni	ENSMUSG00000047039_CHOF:177-186	+	AAAGAAGAAT	–	ATTCTTCTTT
ENSMUSG00000047039_DNOV	Orthologue	Dasypus novemcinctus	scaffold_18954:4,453-4,462	–	AAATATCAAT	+	ATTGATATTT
ENSMUSG00000047039_DRER	Orthologue	Danio rerio	chr10:33,663,140-33,663,149	–	AAATATTATT	+	AATAATATTT
ENSMUSG00000047039_EEUR	Orthologue	Erinaceus europaeus	ENSMUSG00000047039_EEUR:9-18	+	ACAGATCATT	–	AATGATCTGT
ENSMUSG00000047039_GGAL	Orthologue	Gallus gallus	chr5:2,410,104-2,410,113	–	AAATAAGATT	+	AATCTTATTT
ENSMUSG00000047039_HSAP	Orthologue	Homo sapiens	chr11:55,439,777-55,439,786	+	AAATATCATT	–	AATGATATTT
ENSMUSG00000047039_LAFR	Orthologue	Loxodonta africana	scaffold_1215:48,007-48,016	+	AAATATCAAT	–	ATTGATATTT
ENSMUSG00000047039_MDOM	Orthologue	Monodelphis domestica	scaffold_33:16,678,489-16,678,498	–	AAATAACATT	+	AATGTTATTT
ENSMUSG00000047039_MMUL	Orthologue	Macaca mulatta	SCAFFOLD115116:156,361-156,370	+	AAATAACAAT	–	ATTGTTATTT
ENSMUSG00000047039_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_108611:595-604	+	AAAGAAGAAT	–	ATTCTTCTTT
ENSMUSG00000047039_PTRO	Orthologue	Pan troglodytes	9_random:27,082,698-27,082,707	+	AAATATCATT	–	AATGATATTT
ENSMUSG00000047039_RNOR	Orthologue	Rattus norvegicus	chr3:71,559,462-71,559,471	+	AAATAATATT	–	AATATTATTT
ENSMUSG00000047039_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000047039_TBEL:114-123	+	AAAGAAGAAT	–	ATTCTTCTTT
ENSMUSG00000047039_XTRO	Orthologue	Xenopus tropicalis	scaffold_10:4,059,680-4,059,689	+	AAATTTCATT	–	AATGAAATTT

Export Site Sequences Stack