cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000049969 > craMmus348636

Motif craMmus348636

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	craMmus348636
Discovery p-value	3.39E-02
Motif location	chr4: 10,936,210-10,936,217 (-) (8 bp)
Search region location	chr4: 10,934,518-10,937,039 (-) (2,522 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	8 species: Mus musculus, Bos taurus, Homo sapiens, Loxodonta africana, Macaca mulatta, Oryctolagus cuniculus, Pan troglodytes, Rattus norvegicus
Found with	Consensus.oops
'De Novo' motif group ID	This motif was not submitted for clustering.
Similar to (annotation p-value)	There are 4 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (2 annot.): HFH-1(3.33E-04) , Pax-2(8.26E-04) ORegAnno: (2 annot.): FoxA1(2.99E-06) , FoxA1(8.51E-04)
Modules (Co-occurring motif patterns)	No annotation-based modules contain this motif. No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

TTGTTTAA

TTAAACAA

Position frequency matrix

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

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8
A	0	0	8	8	8	0	8	8
C	0	0	0	0	0	7	0	0
G	0	0	0	0	0	1	0	0
T	8	8	0	0	0	0	0	0
	T	T	A	A	A	C	A	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
ENSMUSG00000049969	Target	Mus musculus	chr4:10,936,210-10,936,217	+	TTGTTTAA	–	TTAAACAA
ENSMUSG00000049969_BTAU	Orthologue	Bos taurus	chr7:55,936,701-55,936,708	+	TTGTTTAA	–	TTAAACAA
ENSMUSG00000049969_HSAP	Orthologue	Homo sapiens	chr8:96,214,383-96,214,390	+	TTGTTTAA	–	TTAAACAA
ENSMUSG00000049969_LAFR	Orthologue	Loxodonta africana	scaffold_91565:4,588-4,595	+	TTGTTTAA	–	TTAAACAA
ENSMUSG00000049969_MMUL	Orthologue	Macaca mulatta	SCAFFOLD25396:50,911-50,918	+	TTGTTTAA	–	TTAAACAA
ENSMUSG00000049969_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_213036:109,126-109,133	–	TTGTTTAA	+	TTAAACAA
ENSMUSG00000049969_PTRO	Orthologue	Pan troglodytes	chr7:98,447,984-98,447,991	+	TTGTTTAA	–	TTAAACAA
ENSMUSG00000049969_RNOR	Orthologue	Rattus norvegicus	chr5:24,852,083-24,852,090	+	TTCTTTAA	–	TTAAAGAA

Export Site Sequences Stack