cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000042649 > craMmus47560

Motif craMmus47560

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	craMmus47560
Discovery p-value	9.88E-04
Motif location	chr2: 106,233,622-106,233,629 (+) (8 bp)
Search region location	chr2: 106,232,877-106,234,666 (+) (1,790 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	16 species: Mus musculus, Canis familiaris, Dasypus novemcinctus, Echinops telfairi, Felis catus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Myotis lucifugus, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, Procavia capensis, Pongo pygmaeus, Pan troglodytes, Rattus norvegicus
Found with	MotifSampler
'De Novo' motif group ID	This motif was not submitted for clustering.
Similar to (annotation p-value)	There are 10 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (10 annot.): aMEF-2(5.49E-06) , MEF-2A(9.57E-06) , RSRFC4(2.06E-05) , RSRFC4(5.31E-05) , aMEF-2(1.02E-04) ... ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 25 (FOXJ2__Lhx3a) 39 (Cdx-2__HOXA5) 55 (Lhx3a__aMEF-2) 91 (Cdx-2__RSRFC4) 138 (FOXJ2__RSRFC4) 178 (Lhx3a__RSRFC4) 180 (CUTL1__HOXA5) 271 (CUTL1__RSRFC4) 292 (Cdx-2__aMEF-2) 372 (FOXJ2__FOXJ2) 566 (FOXJ2__Nkx6-2) 787 (CUTL1__aMEF-2) 887 (CUTL1__FOXJ2) 1025 (HOXA5__Lhx3a) 1032 (Lhx3a__Nkx6-2) 1046 (Cdx-2__FOXJ2) 1079 (FOXJ2__HOXA5) 1119 (Lhx3a__MEF-2A) 1151 (FOXJ2__MEF-2A) 1231 (Cdx-2__MEF-2A) 1255 (Cdx-2__Nkx6-2) 1358 (CUTL1__Nkx6-2) 1407 (CUTL1__MEF-2A) 1564 (FOXJ2__aMEF-2) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

ATTATTTT

AAAATAAT

Position frequency matrix

	1	2	3	4	5	6	7	8
A	16	0	0	16	0	0	0	0
C	0	0	0	0	0	1	0	0
G	0	0	0	0	5	0	0	0
T	0	16	16	0	11	15	16	16
	A	T	T	A	T	T	T	T

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8
A	16	16	15	11	0	16	16	0
C	0	0	0	5	0	0	0	0
G	0	0	1	0	0	0	0	0
T	0	0	0	0	16	0	0	16
	A	A	A	A	T	A	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
ENSMUSG00000042649	Target	Mus musculus	chr2:106,233,622-106,233,629	+	ATTATTTT	–	AAAATAAT
ENSMUSG00000042649_CFAM	Orthologue	Canis familiaris	chr18:39,511,899-39,511,906	+	ATTATTTT	–	AAAATAAT
ENSMUSG00000042649_DNOV	Orthologue	Dasypus novemcinctus	scaffold_6300:49,775-49,782	–	ATTATTTT	+	AAAATAAT
ENSMUSG00000042649_ETEL	Orthologue	Echinops telfairi	scaffold_319434:68,477-68,484	–	ATTATTTT	+	AAAATAAT
ENSMUSG00000042649_FCAT	Orthologue	Felis catus	ENSMUSG00000042649_FCAT:191-198	+	ATTAGTTT	–	AAACTAAT
ENSMUSG00000042649_HSAP	Orthologue	Homo sapiens	chr11:30,873,651-30,873,658	–	ATTATTTT	+	AAAATAAT
ENSMUSG00000042649_LAFR	Orthologue	Loxodonta africana	scaffold_285:117,707-117,714	–	ATTATTTT	+	AAAATAAT
ENSMUSG00000042649_MDOM	Orthologue	Monodelphis domestica	scaffold_10:76,880,319-76,880,326	–	ATTATTTT	+	AAAATAAT
ENSMUSG00000042649_MLUC	Orthologue	Myotis lucifugus	ENSMUSG00000042649_MLUC:228-235	–	ATTAGTTT	+	AAACTAAT
ENSMUSG00000042649_MMUL	Orthologue	Macaca mulatta	SCAFFOLD25083:161,364-161,371	+	ATTATTTT	–	AAAATAAT
ENSMUSG00000042649_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_200560:166,456-166,463	–	ATTATTTT	+	AAAATAAT
ENSMUSG00000042649_OGAR	Orthologue	Otolemur garnettii	ENSMUSG00000042649_OGAR:262-269	–	ATTAGTTT	+	AAACTAAT
ENSMUSG00000042649_PCAP	Orthologue	Procavia capensis	ENSMUSG00000042649_PCAP:254-261	–	ATTAGCTT	+	AAGCTAAT
ENSMUSG00000042649_PPYG	Orthologue	Pongo pygmaeus	ENSMUSG00000042649_PPYG:267-274	–	ATTAGTTT	+	AAACTAAT
ENSMUSG00000042649_PTRO	Orthologue	Pan troglodytes	chr9:31,222,677-31,222,684	–	ATTATTTT	+	AAAATAAT
ENSMUSG00000042649_RNOR	Orthologue	Rattus norvegicus	chr3:91,775,310-91,775,317	+	ATTATTTT	–	AAAATAAT

Export Site Sequences Stack