cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000044213 > craMmus223148

Motif craMmus223148

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	craMmus223148
Discovery p-value	2.79E-03
Motif location	chr2: 86,671,892-86,671,903 (+) (12 bp)
Search region location	chr2: 86,670,834-86,672,669 (+) (1,836 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	16 species: Mus musculus, Bos taurus, Canis familiaris, Callithrix jacchus, Cavia porcellus, Dasypus novemcinctus, Danio rerio, Echinops telfairi, Homo sapiens, Loxodonta africana, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, Pan troglodytes, Rattus norvegicus, Xenopus tropicalis
Found with	MotifSampler
'De Novo' motif group ID	This motif was not submitted for clustering.
Similar to (annotation p-value)	There are 9 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (9 annot.): POU1F1(5.72E-05) , FOXP1a(7.59E-05) , IRF-7A(8.07E-05) , IRF-1(9.94E-05) , POU2F1(5.85E-04) ... ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 3 (IRF-1__aMEF-2) 53 (POU1F1__aMEF-2) 72 (FOXP1a__HNF-1alpha) 137 (IRF-7A__aMEF-2) 152 (HNF-1alpha__IRF-7A) 176 (C-EBPgamma__POU1F1) 300 (IRF-7A__MEF-2A) 355 (FOXP1a__aMEF-2) 363 (IRF-1__POU3F1) 533 (POU1F1__POU3F1) 570 (C-EBPgamma__IRF-1) 676 (FOXP1a__RSRFC4) 784 (IRF-7A__POU3F1) 1111 (IRF-7A__RSRFC4) 1192 (C-EBPgamma__FOXP1a) 1259 (FOXP1a__MEF-2A) 1275 (IRF-1__MEF-2A) 1292 (C-EBPgamma__IRF-7A) 1363 (POU1F1__RSRFC4) 1446 (IRF-1__RSRFC4) 1485 (FOXP1a__POU3F1) 1514 (HNF-1alpha__IRF-1) 1543 (AR__POU1F1) 1584 (MEF-2A__POU1F1) 1600 (HNF-1alpha__POU1F1) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

ATTTTTmmTwTT

AAsAkkAAAAAT

Position frequency matrix

	1	2	3	4	5	6	7	8	9	10	11	12
A	12	0	2	0	0	0	8	8	1	10	0	2
C	4	0	0	0	0	0	6	7	0	0	0	0
G	0	0	0	0	0	1	2	0	0	0	0	0
T	0	16	14	16	16	15	0	1	15	6	16	14
	A	T	T	T	T	T	m	m	T	n	T	T

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8	9	10	11	12
A	14	16	6	15	1	0	15	16	16	14	16	0
C	0	0	0	0	0	2	1	0	0	0	0	0
G	0	0	0	0	7	6	0	0	0	0	0	4
T	2	0	10	1	8	8	0	0	0	2	0	12
	A	A	n	A	k	k	A	A	A	A	A	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
ENSMUSG00000044213	Target	Mus musculus	chr2:86,671,892-86,671,903	+	ATTTTTCATTTT	–	AAAATGAAAAAT
ENSMUSG00000044213_BTAU	Orthologue	Bos taurus	chr2:620,589-620,600	–	ATTTTTACTATT	+	AATAGTAAAAAT
ENSMUSG00000044213_CFAM	Orthologue	Canis familiaris	chr18:42,796,123-42,796,134	+	ATTTTTACTATT	–	AATAGTAAAAAT
ENSMUSG00000044213_CJAC	Orthologue	Callithrix jacchus	ENSMUSG00000044213_CJAC:131-142	–	ATTTTTAATATT	+	AATATTAAAAAT
ENSMUSG00000044213_CPOR	Orthologue	Cavia porcellus	ENSMUSG00000044213_CPOR:826-837	+	ATTTTTCCTATT	–	AATAGGAAAAAT
ENSMUSG00000044213_DNOV	Orthologue	Dasypus novemcinctus	scaffold_4603:23,624-23,635	–	CTTTTTCATTTT	+	AAAATGAAAAAG
ENSMUSG00000044213_DRER	Orthologue	Danio rerio	chr15:35,872,464-35,872,475	–	ATATTGGATATT	+	AATATCCAATAT
ENSMUSG00000044213_ETEL	Orthologue	Echinops telfairi	scaffold_75971:2,021-2,032	–	CTTTTTATTATT	+	AATAATAAAAAG
ENSMUSG00000044213_HSAP	Orthologue	Homo sapiens	chr11:55,798,514-55,798,525	+	ATTTTTGATATA	–	TATATCAAAAAT
ENSMUSG00000044213_LAFR	Orthologue	Loxodonta africana	scaffold_806:105,280-105,291	+	CTTTTTACTATT	–	AATAGTAAAAAG
ENSMUSG00000044213_MMUL	Orthologue	Macaca mulatta	SCAFFOLD46343:29,506-29,517	–	ATTTTTACTATT	+	AATAGTAAAAAT
ENSMUSG00000044213_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_173848:42,657-42,668	–	ATTTTTACTTTT	+	AAAAGTAAAAAT
ENSMUSG00000044213_OGAR	Orthologue	Otolemur garnettii	ENSMUSG00000044213_OGAR:141-152	+	ATTTTTCCTTTT	–	AAAAGGAAAAAT
ENSMUSG00000044213_PTRO	Orthologue	Pan troglodytes	chr9:56,647,385-56,647,396	–	ATTTTTCATTTA	+	TAAATGAAAAAT
ENSMUSG00000044213_RNOR	Orthologue	Rattus norvegicus	chr3:69,863,742-69,863,753	+	ATTTTTCATTTT	–	AAAATGAAAAAT
ENSMUSG00000044213_XTRO	Orthologue	Xenopus tropicalis	scaffold_10:3,516,001-3,516,012	+	CTATTTAAAATT	–	AATTTTAAATAG

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