cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000071157 > craMmus443303

Motif craMmus443303

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	craMmus443303
Discovery p-value	7.37E-02
Motif location	chr17: 30,252,398-30,252,405 (+) (8 bp)
Search region location	chr17: 30,252,039-30,253,916 (+) (1,878 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	6 species: Mus musculus, Homo sapiens, Macaca mulatta, Otolemur garnettii, Pan troglodytes, Rattus norvegicus
Found with	Consensus.omops, Consensus.oops
'De Novo' motif group ID	This motif was not submitted for clustering.
Similar to (annotation p-value)	There are 1 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (1 annot.): HOXA5(1.11E-05) ORegAnno: (0 annot.): none
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

swGCTGCC

GGCAGCsw

Position frequency matrix

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

Transfac

Jaspar

CSV

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

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
ENSMUSG00000071157	Target	Mus musculus	chr17:30,252,398-30,252,405	+	CTGCTGCC	–	GGCAGCAG
ENSMUSG00000071157_HSAP	Orthologue	Homo sapiens	chr21:43,938,555-43,938,562	–	GAGCTGCC	+	GGCAGCTC
ENSMUSG00000071157_MMUL	Orthologue	Macaca mulatta	SCAFFOLD35707:3,320-3,327	+	GAGCTGCC	–	GGCAGCTC
ENSMUSG00000071157_OGAR	Orthologue	Otolemur garnettii	ENSMUSG00000071157_OGAR:322-329	+	CTGCTGCC	–	GGCAGCAG
ENSMUSG00000071157_PTRO	Orthologue	Pan troglodytes	chr22:44,060,857-44,060,864	–	GAGCTGCC	+	GGCAGCTC
ENSMUSG00000071157_RNOR	Orthologue	Rattus norvegicus	chr20:10,478,327-10,478,334	+	CTGCTGCC	–	GGCAGCAG

Export Site Sequences Stack