cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000057149 > craMmus392506

Motif craMmus392506

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	craMmus392506
Discovery p-value	2.79E-03
Motif location	chr2: 111,604,453-111,604,462 (+) (10 bp)
Search region location	chr2: 111,603,538-111,605,237 (+) (1,700 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	17 species: Mus musculus, Canis familiaris, Callithrix jacchus, Dasypus novemcinctus, Danio rerio, Equus caballus, Felis catus, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Rattus norvegicus, Sorex araneus, Sus scrofa, 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.): POU6F1_(c2)(7.06E-05) , FOXJ2(1.46E-04) , POU3F2(2.06E-04) , HOXA5(8.06E-04) ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 194 (POU3F2__Pax-8) 210 (FOXJ2__HNF-1alpha) 222 (POU6F1_(c2)__YY1) 268 (FOXJ2__IRF-7A) 285 (HNF-1alpha__POU6F1_(c2)) 372 (FOXJ2__FOXJ2) 562 (POU3F2__YY1) 731 (POU3F2__Pbx) 1016 (FOXJ2__POU6F1_(c2)) 1096 (FOXJ2__YY1) 1201 (IRF-7A__POU3F2) 1233 (FOXJ2__POU3F2) 1263 (POU6F1_(c2)__Pax-8) 1474 (IRF-7A__POU6F1_(c2)) 1476 (HNF-1alpha__POU3F2) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

ATATTkwAwT

AsTsmAATAT

Position frequency matrix

	1	2	3	4	5	6	7	8	9	10
A	17	3	16	0	2	0	10	17	8	0
C	0	0	1	0	0	4	0	0	0	0
G	0	0	0	0	1	7	0	0	0	0
T	0	14	0	17	14	6	7	0	9	17
	A	T	A	T	T	k	w	A	w	T

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8	9	10
A	17	9	0	7	6	14	17	0	14	0
C	0	0	0	0	7	1	0	0	0	0
G	0	0	0	0	4	0	0	1	0	0
T	0	8	17	10	0	2	0	16	3	17
	A	w	T	w	m	A	A	T	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
ENSMUSG00000057149	Target	Mus musculus	chr2:111,604,453-111,604,462	+	ATATTTTAAT	–	ATTAAAATAT
ENSMUSG00000057149_CFAM	Orthologue	Canis familiaris	chr10:19,274,824-19,274,833	+	AAATTTAAAT	–	ATTTAAATTT
ENSMUSG00000057149_CJAC	Orthologue	Callithrix jacchus	ENSMUSG00000057149_CJAC:280-289	–	ATATAGTATT	+	AATACTATAT
ENSMUSG00000057149_DNOV	Orthologue	Dasypus novemcinctus	scaffold_89437:3,213-3,222	–	ATATTTTAAT	+	ATTAAAATAT
ENSMUSG00000057149_DRER	Orthologue	Danio rerio	chr15:35,977,957-35,977,966	+	ATATTTAAAT	–	ATTTAAATAT
ENSMUSG00000057149_ECAB	Orthologue	Equus caballus	ENSMUSG00000057149_ECAB:114-123	–	ATATTGAAAT	+	ATTTCAATAT
ENSMUSG00000057149_FCAT	Orthologue	Felis catus	ENSMUSG00000057149_FCAT:75-84	–	AAATTCTATT	+	AATAGAATTT
ENSMUSG00000057149_GGAL	Orthologue	Gallus gallus	chr5:2,410,038-2,410,047	+	AAATTCAAAT	–	ATTTGAATTT
ENSMUSG00000057149_HSAP	Orthologue	Homo sapiens	chr14:19,554,081-19,554,090	+	ATATTGAAAT	–	ATTTCAATAT
ENSMUSG00000057149_LAFR	Orthologue	Loxodonta africana	scaffold_3200:115,538-115,547	–	ATATTGAATT	+	AATTCAATAT
ENSMUSG00000057149_MDOM	Orthologue	Monodelphis domestica	scaffold_12:31,911,566-31,911,575	–	ATATTCAATT	+	AATTGAATAT
ENSMUSG00000057149_MMUL	Orthologue	Macaca mulatta	SCAFFOLD118315:530-539	–	ATATAGTATT	+	AATACTATAT
ENSMUSG00000057149_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_128745:691-700	–	ATATTCAAAT	+	ATTTGAATAT
ENSMUSG00000057149_RNOR	Orthologue	Rattus norvegicus	chr3:97,197,928-97,197,937	–	ATATTGAATT	+	AATTCAATAT
ENSMUSG00000057149_SARA	Orthologue	Sorex araneus	ENSMUSG00000057149_SARA:239-248	–	ATCTTTTATT	+	AATAAAAGAT
ENSMUSG00000057149_SSCR	Orthologue	Sus scrofa	ENSMUSG00000057149_SSCR:163-172	–	ATATGTAATT	+	AATTACATAT
ENSMUSG00000057149_XTRO	Orthologue	Xenopus tropicalis	scaffold_786:552,544-552,553	+	ATATTGTATT	–	AATACAATAT

Export Site Sequences Stack