cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000060422 > craMmus413272

Motif craMmus413272

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	craMmus413272
Discovery p-value	2.79E-03
Motif location	chr2: 85,889,932-85,889,937 (+) (6 bp)
Search region location	chr2: 85,888,700-85,890,399 (+) (1,700 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	21 species: Mus musculus, Bos taurus, Canis familiaris, Cavia porcellus, Dasypus novemcinctus, Equus caballus, Erinaceus europaeus, Echinops telfairi, Fugu rubripes, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, Procavia capensis, Pan troglodytes, Rattus norvegicus, Sus scrofa, 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: (5 annot.): POU3F2(1.09E-04) , HNF-6(1.39E-04) , COMP1(2.76E-04) , AIRE(7.39E-04) , Chx10(9.56E-04) ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 15 (COMP1__HNF-1alpha) 50 (HNF-1alpha__HNF-6) 66 (E4BP4__HNF-6) 87 (COMP1__HNF-6) 145 (COMP1__POU3F2) 223 (HNF-3__HNF-6) 252 (POU3F2__POU3F2) 280 (COMP1__RSRFC4) 434 (COMP1__POU2F1) 476 (E4BP4__POU3F2) 488 (HNF-6__POU3F2) 511 (COMP1__HNF-3) 584 (COMP1__COMP1) 759 (HNF-6__POU2F1) 808 (AR__POU3F2) 837 (COMP1__E4BP4) 858 (HNF-3__POU3F2) 944 (POU3F2__RSRFC4) 998 (POU2F1__POU3F2) 1047 (HNF-6__RSRFC4) 1070 (AR__COMP1) 1476 (HNF-1alpha__POU3F2) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

TAAATT

AATTTA

Position frequency matrix

	1	2	3	4	5	6
A	0	18	21	21	0	0
C	0	0	0	0	0	0
G	0	3	0	0	0	0
T	21	0	0	0	21	21
	T	A	A	A	T	T

Transfac

Jaspar

CSV

	1	2	3	4	5	6
A	21	21	0	0	0	21
C	0	0	0	0	3	0
G	0	0	0	0	0	0
T	0	0	21	21	18	0
	A	A	T	T	T	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
ENSMUSG00000060422	Target	Mus musculus	chr2:85,889,932-85,889,937	+	TAAATT	–	AATTTA
ENSMUSG00000060422_BTAU	Orthologue	Bos taurus	chr1:22,332,935-22,332,940	–	TAAATT	+	AATTTA
ENSMUSG00000060422_CFAM	Orthologue	Canis familiaris	chr18:42,535,498-42,535,503	–	TAAATT	+	AATTTA
ENSMUSG00000060422_CPOR	Orthologue	Cavia porcellus	ENSMUSG00000060422_CPOR:337-342	–	TGAATT	+	AATTCA
ENSMUSG00000060422_DNOV	Orthologue	Dasypus novemcinctus	scaffold_11091:51,238-51,243	+	TAAATT	–	AATTTA
ENSMUSG00000060422_ECAB	Orthologue	Equus caballus	ENSMUSG00000060422_ECAB:198-203	–	TAAATT	+	AATTTA
ENSMUSG00000060422_EEUR	Orthologue	Erinaceus europaeus	ENSMUSG00000060422_EEUR:129-134	–	TAAATT	+	AATTTA
ENSMUSG00000060422_ETEL	Orthologue	Echinops telfairi	scaffold_288839:83,387-83,392	–	TAAATT	+	AATTTA
ENSMUSG00000060422_FRUB	Orthologue	Fugu rubripes	chrUn:265,469,175-265,469,180	–	TAAATT	+	AATTTA
ENSMUSG00000060422_HSAP	Orthologue	Homo sapiens	chr11:55,988,848-55,988,853	+	TAAATT	–	AATTTA
ENSMUSG00000060422_LAFR	Orthologue	Loxodonta africana	scaffold_2:417,888-417,893	–	TAAATT	+	AATTTA
ENSMUSG00000060422_MDOM	Orthologue	Monodelphis domestica	scaffold_33:19,162,707-19,162,712	+	TAAATT	–	AATTTA
ENSMUSG00000060422_MMUL	Orthologue	Macaca mulatta	SCAFFOLD31127:17,509-17,514	–	TAAATT	+	AATTTA
ENSMUSG00000060422_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_170560:9,971-9,976	+	TAAATT	–	AATTTA
ENSMUSG00000060422_OGAR	Orthologue	Otolemur garnettii	ENSMUSG00000060422_OGAR:82-87	–	TGAATT	+	AATTCA
ENSMUSG00000060422_PCAP	Orthologue	Procavia capensis	ENSMUSG00000060422_PCAP:202-207	–	TGAATT	+	AATTCA
ENSMUSG00000060422_PTRO	Orthologue	Pan troglodytes	chr9:57,011,805-57,011,810	–	TAAATT	+	AATTTA
ENSMUSG00000060422_RNOR	Orthologue	Rattus norvegicus	chr3:69,138,099-69,138,104	–	TAAATT	+	AATTTA
ENSMUSG00000060422_SSCR	Orthologue	Sus scrofa	ENSMUSG00000060422_SSCR:166-171	–	TAAATT	+	AATTTA
ENSMUSG00000060422_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000060422_TBEL:38-43	–	TAAATT	+	AATTTA
ENSMUSG00000060422_XTRO	Orthologue	Xenopus tropicalis	scaffold_10:4,652,169-4,652,174	+	TAAATT	–	AATTTA

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