cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000004698 > craMmus10807

Motif craMmus10807

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	craMmus10807
Discovery p-value	2.79E-03
Motif location	chr12: 32,372,395-32,372,404 (-) (10 bp)
Search region location	chr12: 32,371,748-32,373,478 (-) (1,731 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	25 species: Mus musculus, Bos taurus, Canis familiaris, Callithrix jacchus, Cavia porcellus, Dasypus novemcinctus, Equus caballus, Erinaceus europaeus, Echinops telfairi, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macropus eugenii, Myotis lucifugus, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, Procavia capensis, Pongo pygmaeus, Pan troglodytes, Rattus norvegicus, Sorex araneus, 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.): Cdx-2(8.84E-05) , aMEF-2(3.09E-04) , AIRE(4.83E-04) , Cdc5(6.84E-04) , TFIIA(7.54E-04) ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 53 (POU1F1__aMEF-2) 91 (Cdx-2__RSRFC4) 224 (RORalpha2__aMEF-2) 292 (Cdx-2__aMEF-2) 340 (Cdx-2__POU3F2) 399 (POU3F2__aMEF-2) 934 (RSRFC4__aMEF-2) 938 (C-EBPgamma__aMEF-2) 986 (MEF-2A__aMEF-2) 1044 (Cdx-2__POU1F1) 1231 (Cdx-2__MEF-2A) 1468 (C-EBPgamma__Cdx-2) 1504 (aMEF-2__aMEF-2) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

TsCsAAAATA

TATTTTwGwA

Position frequency matrix

	1	2	3	4	5	6	7	8	9	10
A	5	10	0	10	25	25	25	25	0	25
C	0	0	25	0	0	0	0	0	0	0
G	0	0	0	0	0	0	0	0	0	0
T	20	15	0	15	0	0	0	0	25	0
	T	w	C	w	A	A	A	A	T	A

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8	9	10
A	0	25	0	0	0	0	15	0	15	20
C	0	0	0	0	0	0	0	0	0	0
G	0	0	0	0	0	0	0	25	0	0
T	25	0	25	25	25	25	10	0	10	5
	T	A	T	T	T	T	w	G	w	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
ENSMUSG00000004698	Target	Mus musculus	chr12:32,372,395-32,372,404	+	TTCTAAAATA	–	TATTTTAGAA
ENSMUSG00000004698_BTAU	Orthologue	Bos taurus	chr4:9,126,071-9,126,080	+	TTCTAAAATA	–	TATTTTAGAA
ENSMUSG00000004698_CFAM	Orthologue	Canis familiaris	chr14:35,738,516-35,738,525	–	TTCTAAAATA	+	TATTTTAGAA
ENSMUSG00000004698_CJAC	Orthologue	Callithrix jacchus	ENSMUSG00000004698_CJAC:666-675	–	TTCTAAAATA	+	TATTTTAGAA
ENSMUSG00000004698_CPOR	Orthologue	Cavia porcellus	ENSMUSG00000004698_CPOR:519-528	–	TTCTAAAATA	+	TATTTTAGAA
ENSMUSG00000004698_DNOV	Orthologue	Dasypus novemcinctus	scaffold_30908:16,859-16,868	+	TTCTAAAATA	–	TATTTTAGAA
ENSMUSG00000004698_ECAB	Orthologue	Equus caballus	ENSMUSG00000004698_ECAB:724-733	+	AACAAAAATA	–	TATTTTTGTT
ENSMUSG00000004698_EEUR	Orthologue	Erinaceus europaeus	ENSMUSG00000004698_EEUR:303-312	+	AACAAAAATA	–	TATTTTTGTT
ENSMUSG00000004698_ETEL	Orthologue	Echinops telfairi	scaffold_312460:46,208-46,217	–	TTCTAAAATA	+	TATTTTAGAA
ENSMUSG00000004698_HSAP	Orthologue	Homo sapiens	chr7:18,308,157-18,308,166	–	TTCTAAAATA	+	TATTTTAGAA
ENSMUSG00000004698_LAFR	Orthologue	Loxodonta africana	scaffold_22616:38,582-38,591	+	TTCTAAAATA	–	TATTTTAGAA
ENSMUSG00000004698_MDOM	Orthologue	Monodelphis domestica	scaffold_57:8,398,983-8,398,992	–	AACAAAAATA	+	TATTTTTGTT
ENSMUSG00000004698_MEUG	Orthologue	Macropus eugenii	ENSMUSG00000004698_MEUG:123-132	+	AACAAAAATA	–	TATTTTTGTT
ENSMUSG00000004698_MLUC	Orthologue	Myotis lucifugus	ENSMUSG00000004698_MLUC:344-353	–	TTCTAAAATA	+	TATTTTAGAA
ENSMUSG00000004698_MMUL	Orthologue	Macaca mulatta	SCAFFOLD90617:54,155-54,164	–	TTCTAAAATA	+	TATTTTAGAA
ENSMUSG00000004698_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_205187:52,094-52,103	–	TTCTAAAATA	+	TATTTTAGAA
ENSMUSG00000004698_OGAR	Orthologue	Otolemur garnettii	ENSMUSG00000004698_OGAR:438-447	+	TACAAAAATA	–	TATTTTTGTA
ENSMUSG00000004698_PCAP	Orthologue	Procavia capensis	ENSMUSG00000004698_PCAP:875-884	+	TACAAAAATA	–	TATTTTTGTA
ENSMUSG00000004698_PPYG	Orthologue	Pongo pygmaeus	ENSMUSG00000004698_PPYG:367-376	–	TTCTAAAATA	+	TATTTTAGAA
ENSMUSG00000004698_PTRO	Orthologue	Pan troglodytes	chr6:19,214,186-19,214,195	–	TTCTAAAATA	+	TATTTTAGAA
ENSMUSG00000004698_RNOR	Orthologue	Rattus norvegicus	chr6:53,203,325-53,203,334	+	TTCTAAAATA	–	TATTTTAGAA
ENSMUSG00000004698_SARA	Orthologue	Sorex araneus	ENSMUSG00000004698_SARA:422-431	+	TACAAAAATA	–	TATTTTTGTA
ENSMUSG00000004698_SSCR	Orthologue	Sus scrofa	ENSMUSG00000004698_SSCR:304-313	+	AACAAAAATA	–	TATTTTTGTT
ENSMUSG00000004698_STRI	Orthologue	Spermophilus tridecemlineatus	ENSMUSG00000004698_STRI:128-137	+	TACAAAAATA	–	TATTTTTGTA
ENSMUSG00000004698_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000004698_TBEL:223-232	+	TACAAAAATA	–	TATTTTTGTA

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