cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000059319 > craMmus405218

Motif craMmus405218

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	craMmus405218
Discovery p-value	2.79E-03
Motif location	chr7: 82,520,172-82,520,178 (+) (7 bp)
Search region location	chr7: 82,518,620-82,520,634 (+) (2,015 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	12 species: Mus musculus, Canis familiaris, Dasypus novemcinctus, Danio rerio, Echinops telfairi, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Pan troglodytes, Rattus norvegicus, 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.): HOXA5(1.48E-04) , Pax-6(8.39E-04) ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 204 (HOXA5__HOXA5) 333 (HOXA5__HP1_site_factor) 361 (HOXA5__POU3F2) 438 (HOXA5__POU2F1) 687 (HOXA5__Pax-6) 699 (HOXA5__SRF) 875 (HOXA5__Nkx6-2) 904 (HOXA5__IPF1) 1025 (HOXA5__Lhx3a) 1412 (FOXP1a__HOXA5) 1439 (Evi-1__HOXA5) 1464 (HOXA5__aMEF-2) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

TTCATAn

nTATGAA

Position frequency matrix

	1	2	3	4	5	6	7
A	0	1	0	12	0	12	3
C	0	0	12	0	0	0	2
G	0	0	0	0	0	0	2
T	12	11	0	0	12	0	5
	T	T	C	A	T	A	n

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7
A	5	0	12	0	0	11	12
C	2	0	0	0	0	0	0
G	2	0	0	0	12	0	0
T	3	12	0	12	0	1	0
	n	T	A	T	G	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
ENSMUSG00000059319	Target	Mus musculus	chr7:82,520,172-82,520,178	+	TTCATAT	–	ATATGAA
ENSMUSG00000059319_CFAM	Orthologue	Canis familiaris	chr14:5,334,068-5,334,074	–	TTCATAA	+	TTATGAA
ENSMUSG00000059319_DNOV	Orthologue	Dasypus novemcinctus	scaffold_39105:4,134-4,140	+	TTCATAG	–	CTATGAA
ENSMUSG00000059319_DRER	Orthologue	Danio rerio	chr21:38,717,731-38,717,737	+	TTCATAT	–	ATATGAA
ENSMUSG00000059319_ETEL	Orthologue	Echinops telfairi	scaffold_267478:3,500-3,506	–	TTCATAT	+	ATATGAA
ENSMUSG00000059319_HSAP	Orthologue	Homo sapiens	chr1:244,836,918-244,836,924	–	TTCATAT	+	ATATGAA
ENSMUSG00000059319_LAFR	Orthologue	Loxodonta africana	scaffold_78794:587-593	–	TACATAA	+	TTATGTA
ENSMUSG00000059319_MDOM	Orthologue	Monodelphis domestica	scaffold_121:3,001,718-3,001,724	–	TTCATAA	+	TTATGAA
ENSMUSG00000059319_MMUL	Orthologue	Macaca mulatta	SCAFFOLD478:4,998-5,004	+	TTCATAG	–	CTATGAA
ENSMUSG00000059319_PTRO	Orthologue	Pan troglodytes	chr1:228,896,564-228,896,570	–	TTCATAT	+	ATATGAA
ENSMUSG00000059319_RNOR	Orthologue	Rattus norvegicus	chr1:142,913,239-142,913,245	–	TTCATAC	+	GTATGAA
ENSMUSG00000059319_XTRO	Orthologue	Xenopus tropicalis	scaffold_7:4,565,391-4,565,397	+	TTCATAC	–	GTATGAA

Export Site Sequences Stack