cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000056648 > craMmus393962

Motif craMmus393962

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	craMmus393962
Discovery p-value	2.79E-03
Motif location	chr11: 96,390,914-96,390,923 (+) (10 bp)
Search region location	chr11: 96,389,405-96,391,143 (+) (1,739 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	24 species: Mus musculus, Bos taurus, Canis familiaris, Callithrix jacchus, Cavia porcellus, Erinaceus europaeus, Echinops telfairi, Felis catus, Gallus gallus, Homo sapiens, Monodelphis domestica, Macropus eugenii, Myotis lucifugus, Macaca mulatta, Oryctolagus cuniculus, Procavia capensis, Pongo pygmaeus, Pan troglodytes, Rattus norvegicus, Sorex araneus, Sus scrofa, Spermophilus tridecemlineatus, 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 5 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (4 annot.): HNF-1alpha(3.60E-04) , C-EBPbeta(5.74E-04) , POU1F1(6.22E-04) , HOXA5(6.90E-04) ORegAnno: (1 annot.): FoxA1(2.76E-04)
Modules (Co-occurring motif patterns)	Annotation-based: 23 (HNF-1alpha__Pax-6) 60 (Cdx-2__HNF-1alpha) 83 (C-EBPalpha__HNF-1alpha) 111 (CUTL1__HNF-1alpha) 152 (HNF-1alpha__IRF-7A) 185 (HNF-1alpha__HNF-3) 215 (HNF-1alpha__YY1) 218 (HNF-1alpha__HOXA3) 479 (Cdc5__HNF-1alpha) 602 (HNF-1alpha__Nkx6-2) 644 (HFH-1__HNF-1alpha) 767 (HNF-1alpha__aMEF-2) 774 (HNF-1alpha__POU2F1) 844 (HNF-1alpha__Msx-1) 1000 (HNF-1alpha__IPF1) 1021 (HNF-1alpha__Sox9) 1147 (HNF-1alpha__S8) 1254 (HNF-1alpha__HNF-1alpha) 1492 (HNF-1alpha__POU3F1) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

CTTTATCAAT

ATTGATAAAG

Position frequency matrix

	1	2	3	4	5	6	7	8	9	10
A	0	3	0	3	24	3	0	24	24	0
C	24	0	0	0	0	0	24	0	0	3
G	0	0	0	0	0	0	0	0	0	0
T	0	21	24	21	0	21	0	0	0	21
	C	T	T	T	A	T	C	A	A	T

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8	9	10
A	21	0	0	0	21	0	21	24	21	0
C	0	0	0	0	0	0	0	0	0	0
G	3	0	0	24	0	0	0	0	0	24
T	0	24	24	0	3	24	3	0	3	0
	A	T	T	G	A	T	A	A	A	G

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
ENSMUSG00000056648	Target	Mus musculus	chr11:96,390,914-96,390,923	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_BTAU	Orthologue	Bos taurus	chr19:31,232,393-31,232,402	–	CTTTATCAAT	+	ATTGATAAAG
ENSMUSG00000056648_CFAM	Orthologue	Canis familiaris	chr9:28,205,282-28,205,291	–	CTTTATCAAT	+	ATTGATAAAG
ENSMUSG00000056648_CJAC	Orthologue	Callithrix jacchus	ENSMUSG00000056648_CJAC:1,564-1,573	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_CPOR	Orthologue	Cavia porcellus	ENSMUSG00000056648_CPOR:309-318	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_EEUR	Orthologue	Erinaceus europaeus	ENSMUSG00000056648_EEUR:86-95	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_ETEL	Orthologue	Echinops telfairi	scaffold_316744:59,822-59,831	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_FCAT	Orthologue	Felis catus	ENSMUSG00000056648_FCAT:360-369	+	CATAAACAAC	–	GTTGTTTATG
ENSMUSG00000056648_GGAL	Orthologue	Gallus gallus	chr27:2,226,666-2,226,675	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_HSAP	Orthologue	Homo sapiens	chr17:44,048,136-44,048,145	–	CTTTATCAAT	+	ATTGATAAAG
ENSMUSG00000056648_MDOM	Orthologue	Monodelphis domestica	scaffold_18:45,581,274-45,581,283	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_MEUG	Orthologue	Macropus eugenii	ENSMUSG00000056648_MEUG:228-237	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_MLUC	Orthologue	Myotis lucifugus	ENSMUSG00000056648_MLUC:631-640	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_MMUL	Orthologue	Macaca mulatta	SCAFFOLD60055:57,722-57,731	–	CTTTATCAAT	+	ATTGATAAAG
ENSMUSG00000056648_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_203826:148,118-148,127	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_PCAP	Orthologue	Procavia capensis	ENSMUSG00000056648_PCAP:475-484	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_PPYG	Orthologue	Pongo pygmaeus	ENSMUSG00000056648_PPYG:635-644	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_PTRO	Orthologue	Pan troglodytes	19_random:42,997,116-42,997,125	–	CTTTATCAAT	+	ATTGATAAAG
ENSMUSG00000056648_RNOR	Orthologue	Rattus norvegicus	chr10:85,027,114-85,027,123	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_SARA	Orthologue	Sorex araneus	ENSMUSG00000056648_SARA:137-146	+	CATAAACAAC	–	GTTGTTTATG
ENSMUSG00000056648_SSCR	Orthologue	Sus scrofa	ENSMUSG00000056648_SSCR:159-168	+	CATAAACAAC	–	GTTGTTTATG
ENSMUSG00000056648_STRI	Orthologue	Spermophilus tridecemlineatus	ENSMUSG00000056648_STRI:368-377	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000056648_TBEL:615-624	+	CTTTATCAAT	–	ATTGATAAAG
ENSMUSG00000056648_XTRO	Orthologue	Xenopus tropicalis	scaffold_329:584,784-584,793	–	CTTTATCAAT	+	ATTGATAAAG

Export Site Sequences Stack