cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000048456 > craMmus345894

Motif craMmus345894

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	craMmus345894
Discovery p-value	2.79E-03
Motif location	chr19: 12,601,427-12,601,436 (-) (10 bp)
Search region location	chr19: 12,600,205-12,602,353 (-) (2,149 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	20 species: Mus musculus, Canis familiaris, Dasypus novemcinctus, Equus caballus, Erinaceus europaeus, Echinops telfairi, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macropus eugenii, Macaca mulatta, Ovis aries, Oryctolagus cuniculus, Otolemur garnettii, Procavia capensis, 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 6 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (6 annot.): Hlf(1.11E-04) , POU2F1(1.29E-04) , C-EBPalpha(3.77E-04) , C-EBPdelta(4.12E-04) , C-EBPbeta(4.14E-04) ... ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 139 (OCA-B__POU2F1) 235 (Hlf__Lhx3a) 272 (Hlf__Nkx6-2) 287 (C-EBPdelta__POU2F1) 295 (POU2F1__Pax-6) 433 (Nkx6-2__POU2F1) 697 (HNF-6__Hlf) 759 (HNF-6__POU2F1) 780 (C-EBPgamma__POU2F1) 785 (Hlf__MEF-2A) 849 (C-EBPbeta__POU2F1) 871 (MEF-2A__POU2F1) 888 (Hlf__OCA-B) 922 (FOXJ2__POU2F1) 942 (POU2F1__POU6F1_(c2)) 998 (POU2F1__POU3F2) 1159 (Hlf__POU2F1) 1180 (POU2F1__POU2F1) 1202 (C-EBPalpha__POU2F1) 1380 (Cdc5__POU2F1) 1382 (Hlf__POU3F2) 1389 (C-EBPalpha__POU3F2) 1431 (FOXJ2__Hlf) 1445 (Lhx3a__POU2F1) 1530 (Hlf__POU6F1_(c2)) 1575 (HNF-4__POU2F1) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

ATsyTrAAsT

AwTTyArwAT

Position frequency matrix

	1	2	3	4	5	6	7	8	9	10
A	20	5	10	4	0	9	17	17	7	0
C	0	2	0	9	0	0	0	0	0	0
G	0	0	0	0	0	11	1	0	0	0
T	0	13	10	7	20	0	2	3	13	20
	A	T	w	y	T	r	A	A	n	T

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8	9	10
A	20	13	3	2	0	20	7	10	13	0
C	0	0	0	1	11	0	0	0	0	0
G	0	0	0	0	0	0	9	0	2	0
T	0	7	17	17	9	0	4	10	5	20
	A	n	T	T	y	A	r	w	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
ENSMUSG00000048456	Target	Mus musculus	chr19:12,601,427-12,601,436	+	ATTATGAAAT	–	ATTTCATAAT
ENSMUSG00000048456_CFAM	Orthologue	Canis familiaris	chr18:40,955,269-40,955,278	+	ATTCTATAAT	–	ATTATAGAAT
ENSMUSG00000048456_DNOV	Orthologue	Dasypus novemcinctus	scaffold_170430:420-429	–	ATTTTAAATT	+	AATTTAAAAT
ENSMUSG00000048456_ECAB	Orthologue	Equus caballus	ENSMUSG00000048456_ECAB:154-163	+	ATACTGAAAT	–	ATTTCAGTAT
ENSMUSG00000048456_EEUR	Orthologue	Erinaceus europaeus	ENSMUSG00000048456_EEUR:3-12	+	ATTCTGAATT	–	AATTCAGAAT
ENSMUSG00000048456_ETEL	Orthologue	Echinops telfairi	scaffold_232072:18,523-18,532	–	AATATAAATT	+	AATTTATATT
ENSMUSG00000048456_FRUB	Orthologue	Fugu rubripes	chrUn:56,752,294-56,752,303	+	ACATTGAATT	–	AATTCAATGT
ENSMUSG00000048456_GGAL	Orthologue	Gallus gallus	chr5:2,425,273-2,425,282	–	ATATTAAAAT	+	ATTTTAATAT
ENSMUSG00000048456_HSAP	Orthologue	Homo sapiens	chr11:57,965,367-57,965,376	–	ATACTAATAT	+	ATATTAGTAT
ENSMUSG00000048456_LAFR	Orthologue	Loxodonta africana	scaffold_109733:5,033-5,042	–	AATCTGAATT	+	AATTCAGATT
ENSMUSG00000048456_MDOM	Orthologue	Monodelphis domestica	scaffold_33:18,375,405-18,375,414	–	ATATTGAATT	+	AATTCAATAT
ENSMUSG00000048456_MEUG	Orthologue	Macropus eugenii	ENSMUSG00000048456_MEUG:1-10	+	ATTCTAATTT	–	AAATTAGAAT
ENSMUSG00000048456_MMUL	Orthologue	Macaca mulatta	SCAFFOLD75060:90,343-90,352	+	ATTTTAAATT	–	AATTTAAAAT
ENSMUSG00000048456_OARI	Orthologue	Ovis aries	ENSMUSG00000048456_OARI:487-496	+	AATCTGAATT	–	AATTCAGATT
ENSMUSG00000048456_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_59244:32-41	+	ATATTGAAAT	–	ATTTCAATAT
ENSMUSG00000048456_OGAR	Orthologue	Otolemur garnettii	ENSMUSG00000048456_OGAR:235-244	+	ATTTTGATTT	–	AAATCAAAAT
ENSMUSG00000048456_PCAP	Orthologue	Procavia capensis	ENSMUSG00000048456_PCAP:40-49	+	AAAATGAATT	–	AATTCATTTT
ENSMUSG00000048456_RNOR	Orthologue	Rattus norvegicus	chr1:216,209,382-216,209,391	–	ATACTAGATT	+	AATCTAGTAT
ENSMUSG00000048456_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000048456_TBEL:18-27	+	ACAATGTATT	–	AATACATTGT
ENSMUSG00000048456_XTRO	Orthologue	Xenopus tropicalis	scaffold_94:2,109,355-2,109,364	+	AAACTAAAAT	–	ATTTTAGTTT

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