cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000062245 > craMmus298447

Motif craMmus298447

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	craMmus298447
Discovery p-value	2.79E-03
Motif location	chr16: 19,158,528-19,158,535 (-) (8 bp)
Search region location	chr16: 19,156,488-19,158,711 (-) (2,224 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	12 species: Mus musculus, Canis familiaris, Choloepus hoffmanni, Callithrix jacchus, Dasypus novemcinctus, Danio rerio, Homo sapiens, Loxodonta africana, Macaca mulatta, Oryctolagus cuniculus, Pan troglodytes, Xenopus tropicalis
Found with	MotifSampler
'De Novo' motif group ID	This motif was not submitted for clustering.
Similar to (annotation p-value)	There are 5 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (5 annot.): Cdx-2(3.77E-04) , FOXD3(3.95E-04) , POU2F1(7.34E-04) , CAR(9.05E-04) , LEF-1(9.83E-04) ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 18 (FOXD3__aMEF-2) 39 (Cdx-2__HOXA5) 60 (Cdx-2__HNF-1alpha) 292 (Cdx-2__aMEF-2) 407 (Cdx-2__SRF) 451 (Cdx-2__Pbx1a) 621 (Cdx-2__TEF) 727 (FOXD3__TEF) 747 (Cdx-2__FOXD3) 825 (Cdx-2__PPAR-alpha) 846 (FOXD3__HNF-1alpha) 916 (Cdx-2__POU2F1) 1034 (FOXD3__POU2F1) 1126 (COMP1__Cdx-2) 1223 (Cdx-2__Pax-6) 1339 (FOXD3__HOXA5) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

ATTTTATT

AATAAAAT

Position frequency matrix

	1	2	3	4	5	6	7	8
A	12	0	0	0	0	11	2	0
C	0	0	0	0	0	1	0	0
G	0	0	0	0	0	0	0	0
T	0	12	12	12	12	0	10	12
	A	T	T	T	T	A	T	T

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8
A	12	10	0	12	12	12	12	0
C	0	0	0	0	0	0	0	0
G	0	0	1	0	0	0	0	0
T	0	2	11	0	0	0	0	12
	A	A	T	A	A	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
ENSMUSG00000062245	Target	Mus musculus	chr16:19,158,528-19,158,535	+	ATTTTATT	–	AATAAAAT
ENSMUSG00000062245_CFAM	Orthologue	Canis familiaris	chr14:4,489,490-4,489,497	–	ATTTTATT	+	AATAAAAT
ENSMUSG00000062245_CHOF	Orthologue	Choloepus hoffmanni	ENSMUSG00000062245_CHOF:333-340	+	ATTTTATT	–	AATAAAAT
ENSMUSG00000062245_CJAC	Orthologue	Callithrix jacchus	ENSMUSG00000062245_CJAC:433-440	+	ATTTTCAT	–	ATGAAAAT
ENSMUSG00000062245_DNOV	Orthologue	Dasypus novemcinctus	scaffold_9381:293-300	–	ATTTTAAT	+	ATTAAAAT
ENSMUSG00000062245_DRER	Orthologue	Danio rerio	chr10:33,564,605-33,564,612	–	ATTTTATT	+	AATAAAAT
ENSMUSG00000062245_HSAP	Orthologue	Homo sapiens	chr1:244,421,942-244,421,949	+	ATTTTATT	–	AATAAAAT
ENSMUSG00000062245_LAFR	Orthologue	Loxodonta africana	scaffold_5551:5,650-5,657	+	ATTTTATT	–	AATAAAAT
ENSMUSG00000062245_MMUL	Orthologue	Macaca mulatta	SCAFFOLD80455:32,507-32,514	–	ATTTTATT	+	AATAAAAT
ENSMUSG00000062245_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_175346:43,228-43,235	+	ATTTTATT	–	AATAAAAT
ENSMUSG00000062245_PTRO	Orthologue	Pan troglodytes	chr1:228,489,248-228,489,255	+	ATTTTATT	–	AATAAAAT
ENSMUSG00000062245_XTRO	Orthologue	Xenopus tropicalis	scaffold_786:296,921-296,928	–	ATTTTATT	+	AATAAAAT

Export Site Sequences Stack