cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000057461 > craMmus290701

Motif craMmus290701

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	craMmus290701
Discovery p-value	2.79E-03
Motif location	chr7: 99,224,256-99,224,263 (-) (8 bp)
Search region location	chr7: 99,222,887-99,224,586 (-) (1,700 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	11 species: Mus musculus, Canis familiaris, Dasypus novemcinctus, Danio rerio, Loxodonta africana, Myotis lucifugus, Oryctolagus cuniculus, Otolemur garnettii, 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 10 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (7 annot.): POU3F2(7.72E-05) , HOXA5(1.48E-04) , POU3F2(4.61E-04) , S8(4.69E-04) , POU1F1(4.86E-04) ... ORegAnno: (3 annot.): FoxA1(2.76E-04) , FoxA1(6.44E-04) , FoxA1(8.55E-04)
Modules (Co-occurring motif patterns)	Annotation-based: 180 (CUTL1__HOXA5) 391 (CUTL1__POU3F2) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

ssmATGAA

TTCATkww

Position frequency matrix

	1	2	3	4	5	6	7	8
A	4	6	4	11	0	0	10	9
C	0	0	7	0	0	0	1	0
G	0	0	0	0	0	11	0	0
T	7	5	0	0	11	0	0	2
	n	w	n	A	T	G	A	A

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8
A	2	0	0	11	0	0	5	7
C	0	0	11	0	0	0	0	0
G	0	1	0	0	0	7	0	0
T	9	10	0	0	11	4	6	4
	T	T	C	A	T	n	w	n

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
ENSMUSG00000057461	Target	Mus musculus	chr7:99,224,256-99,224,263	+	TTAATGAA	–	TTCATTAA
ENSMUSG00000057461_CFAM	Orthologue	Canis familiaris	chr21:30,683,996-30,684,003	–	TACATGAA	+	TTCATGTA
ENSMUSG00000057461_DNOV	Orthologue	Dasypus novemcinctus	scaffold_69027:2,097-2,104	–	TACATGAT	+	ATCATGTA
ENSMUSG00000057461_DRER	Orthologue	Danio rerio	chr10:33,577,255-33,577,262	+	AACATGAA	–	TTCATGTT
ENSMUSG00000057461_LAFR	Orthologue	Loxodonta africana	scaffold_15523:22,052-22,059	–	TACATGAA	+	TTCATGTA
ENSMUSG00000057461_MLUC	Orthologue	Myotis lucifugus	ENSMUSG00000057461_MLUC:182-189	–	TTCATGAA	+	TTCATGAA
ENSMUSG00000057461_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_160364:7,935-7,942	+	TAAATGAA	–	TTCATTTA
ENSMUSG00000057461_OGAR	Orthologue	Otolemur garnettii	ENSMUSG00000057461_OGAR:237-244	–	TTCATGCA	+	TGCATGAA
ENSMUSG00000057461_RNOR	Orthologue	Rattus norvegicus	chr1:161,019,052-161,019,059	+	ATAATGAA	–	TTCATTAT
ENSMUSG00000057461_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000057461_TBEL:299-306	+	ATAATGAT	–	ATCATTAT
ENSMUSG00000057461_XTRO	Orthologue	Xenopus tropicalis	scaffold_1339:155,836-155,843	–	AACATGAA	+	TTCATGTT

Export Site Sequences Stack