cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000056995 > craMmus392050

Motif craMmus392050

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	craMmus392050
Discovery p-value	2.79E-03
Motif location	chr2: 88,234,709-88,234,716 (+) (8 bp)
Search region location	chr2: 88,233,252-88,235,164 (+) (1,913 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	18 species: Mus musculus, Canis familiaris, Choloepus hoffmanni, Dasypus novemcinctus, Danio rerio, Erinaceus europaeus, Echinops telfairi, Felis catus, Fugu rubripes, Homo sapiens, Loxodonta africana, Macaca mulatta, Oryctolagus cuniculus, Pan troglodytes, Rattus norvegicus, Sus scrofa, Spermophilus tridecemlineatus, Tupaia belangeri
Found with	MotifSampler
'De Novo' motif group ID	This motif was not submitted for clustering.
Similar to (annotation p-value)	There are 5 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (5 annot.): POU6F1_(c2)(7.06E-05) , Chx10(2.02E-04) , AFP1(3.32E-04) , POU3F2(5.20E-04) , Pbx1a(9.04E-04) ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 118 (Chx10__Evi-1) 317 (POU6F1_(c2)__aMEF-2) 358 (Chx10__POU2F1) 412 (AFP1__IRF-1) 417 (POU6F1_(c2)__POU6F1_(c2)) 498 (Chx10__HOXA5) 519 (Evi-1__POU6F1_(c2)) 525 (AFP1__Chx10) 611 (Chx10__POU1F1) 700 (AFP1__HOXA5) 740 (AFP1__AIRE) 751 (AFP1__POU2F1) 762 (AFP1__aMEF-2) 914 (Chx10__POU6F1_(c2)) 942 (POU2F1__POU6F1_(c2)) 966 (AIRE__POU6F1_(c2)) 1069 (POU1F1__POU6F1_(c2)) 1143 (AIRE__Chx10) 1175 (AFP1__Evi-1) 1207 (Chx10__IRF-1) 1441 (HOXA5__POU6F1_(c2)) 1471 (Chx10__aMEF-2) 1517 (AFP1__POU1F1) 1534 (AFP1__POU6F1_(c2)) 1599 (IRF-1__POU6F1_(c2)) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

TAAATTmT

AkAATTTA

Position frequency matrix

	1	2	3	4	5	6	7	8
A	0	18	18	17	0	0	9	4
C	0	0	0	0	0	0	9	0
G	0	0	0	0	0	0	0	0
T	18	0	0	1	18	18	0	14
	T	A	A	A	T	T	m	T

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8
A	14	0	18	18	1	0	0	18
C	0	0	0	0	0	0	0	0
G	0	9	0	0	0	0	0	0
T	4	9	0	0	17	18	18	0
	A	k	A	A	T	T	T	A

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
ENSMUSG00000056995	Target	Mus musculus	chr2:88,234,709-88,234,716	+	TAATTTAT	–	ATAAATTA
ENSMUSG00000056995_CFAM	Orthologue	Canis familiaris	chr18:43,240,173-43,240,180	–	TAAATTCT	+	AGAATTTA
ENSMUSG00000056995_CHOF	Orthologue	Choloepus hoffmanni	ENSMUSG00000056995_CHOF:343-350	–	TAAATTCT	+	AGAATTTA
ENSMUSG00000056995_DNOV	Orthologue	Dasypus novemcinctus	scaffold_241924:1,937-1,944	+	TAAATTCT	–	AGAATTTA
ENSMUSG00000056995_DRER	Orthologue	Danio rerio	chr15:35,899,589-35,899,596	+	TAAATTCA	–	TGAATTTA
ENSMUSG00000056995_EEUR	Orthologue	Erinaceus europaeus	ENSMUSG00000056995_EEUR:189-196	–	TAAATTCA	+	TGAATTTA
ENSMUSG00000056995_ETEL	Orthologue	Echinops telfairi	scaffold_7977:4,780-4,787	+	TAAATTAT	–	ATAATTTA
ENSMUSG00000056995_FCAT	Orthologue	Felis catus	ENSMUSG00000056995_FCAT:78-85	–	TAAATTCA	+	TGAATTTA
ENSMUSG00000056995_FRUB	Orthologue	Fugu rubripes	chrUn:304,385,705-304,385,712	–	TAAATTAT	+	ATAATTTA
ENSMUSG00000056995_HSAP	Orthologue	Homo sapiens	chr11:55,162,362-55,162,369	+	TAAATTAT	–	ATAATTTA
ENSMUSG00000056995_LAFR	Orthologue	Loxodonta africana	scaffold_1172:57,741-57,748	–	TAAATTAT	+	ATAATTTA
ENSMUSG00000056995_MMUL	Orthologue	Macaca mulatta	SCAFFOLD5079:109,907-109,914	–	TAAATTAT	+	ATAATTTA
ENSMUSG00000056995_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_126031:2,754-2,761	–	TAAATTAA	+	TTAATTTA
ENSMUSG00000056995_PTRO	Orthologue	Pan troglodytes	chr9:56,063,875-56,063,882	+	TAAATTAT	–	ATAATTTA
ENSMUSG00000056995_RNOR	Orthologue	Rattus norvegicus	chr3:71,985,507-71,985,514	–	TAAATTAT	+	ATAATTTA
ENSMUSG00000056995_SSCR	Orthologue	Sus scrofa	ENSMUSG00000056995_SSCR:215-222	–	TAAATTCT	+	AGAATTTA
ENSMUSG00000056995_STRI	Orthologue	Spermophilus tridecemlineatus	ENSMUSG00000056995_STRI:180-187	–	TAAATTCT	+	AGAATTTA
ENSMUSG00000056995_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000056995_TBEL:562-569	–	TAAATTCT	+	AGAATTTA

Export Site Sequences Stack