cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000070856 > craMmus220085

Motif craMmus220085

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	craMmus220085
Discovery p-value	2.79E-03
Motif location	chr2: 87,095,431-87,095,438 (+) (8 bp)
Search region location	chr2: 87,093,143-87,095,854 (+) (2,712 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	11 species: Mus musculus, Bos taurus, Choloepus hoffmanni, Dasypus novemcinctus, Echinops telfairi, Felis catus, Loxodonta africana, Monodelphis domestica, Rattus norvegicus, 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 2 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (2 annot.): AFP1(1.89E-04) , POU6F1_(c2)(4.70E-04) ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 408 (AFP1__FOXP1a) 751 (AFP1__POU2F1) 792 (AFP1__OCA-B) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

AAAwTATA

TATAsTTT

Position frequency matrix

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

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8
A	0	8	0	11	7	0	0	0
C	0	0	3	0	0	0	0	0
G	0	3	0	0	0	0	0	0
T	11	0	8	0	4	11	11	11
	T	A	T	A	n	T	T	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
ENSMUSG00000070856	Target	Mus musculus	chr2:87,095,431-87,095,438	+	AAAATATA	–	TATATTTT
ENSMUSG00000070856_BTAU	Orthologue	Bos taurus	chr2:605,690-605,697	+	AAATTATA	–	TATAATTT
ENSMUSG00000070856_CHOF	Orthologue	Choloepus hoffmanni	ENSMUSG00000070856_CHOF:287-294	+	AAATTACA	–	TGTAATTT
ENSMUSG00000070856_DNOV	Orthologue	Dasypus novemcinctus	scaffold_56908:423-430	+	AAATTATA	–	TATAATTT
ENSMUSG00000070856_ETEL	Orthologue	Echinops telfairi	scaffold_52200:46-53	+	AAAATACA	–	TGTATTTT
ENSMUSG00000070856_FCAT	Orthologue	Felis catus	ENSMUSG00000070856_FCAT:190-197	+	AAATTGTA	–	TACAATTT
ENSMUSG00000070856_LAFR	Orthologue	Loxodonta africana	scaffold_8581:54,733-54,740	–	AAATTATA	+	TATAATTT
ENSMUSG00000070856_MDOM	Orthologue	Monodelphis domestica	scaffold_33:17,797,589-17,797,596	–	AAATTATA	+	TATAATTT
ENSMUSG00000070856_RNOR	Orthologue	Rattus norvegicus	chr3:70,832,573-70,832,580	–	AAATTGTA	+	TACAATTT
ENSMUSG00000070856_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000070856_TBEL:11-18	+	AAAATGTA	–	TACATTTT
ENSMUSG00000070856_XTRO	Orthologue	Xenopus tropicalis	scaffold_499:82,457-82,464	–	AAAATACA	+	TGTATTTT

Export Site Sequences Stack