cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000070362 > craMmus229956

Motif craMmus229956

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	craMmus229956
Discovery p-value	2.79E-03
Motif location	chr3: 112,974,935-112,974,944 (-) (10 bp)
Search region location	chr3: 112,974,669-112,977,055 (-) (2,387 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	22 species: Mus musculus, Canis familiaris, Choloepus hoffmanni, Callithrix jacchus, Cavia porcellus, Dasypus novemcinctus, Equus caballus, Echinops telfairi, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, Pongo pygmaeus, Pan troglodytes, Sus scrofa, Tupaia belangeri, Tetraodon nigroviridis, Xenopus tropicalis
Found with	MotifSampler
'De Novo' motif group ID	This motif was not submitted for clustering.
Similar to (annotation p-value)	There are 10 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (6 annot.): HNF-6(2.59E-04) , HNF-3(4.18E-04) , FOXJ2(5.41E-04) , HNF-3(5.45E-04) , Sox9(6.45E-04) ... ORegAnno: (4 annot.): FoxA1(6.32E-05) , FoxA1(7.75E-05) , FoxA1(2.76E-04) , FoxA1(4.25E-04)
Modules (Co-occurring motif patterns)	Annotation-based: 50 (HNF-1alpha__HNF-6) 63 (HNF-6__POU1F1) 134 (HNF-6__MEF-2A) 332 (CUTL1__HNF-6) 462 (HNF-6__MRF-2) 468 (HNF-6__POU6F1_(c2)) 1047 (HNF-6__RSRFC4) 1050 (HNF-6__LEF-1) 1106 (HNF-6__aMEF-2) 1438 (FOXJ2__HNF-6) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

AAGTAsAsAT

ATwTwTACTT

Position frequency matrix

	1	2	3	4	5	6	7	8	9	10
A	18	22	4	0	20	11	14	8	22	0
C	0	0	1	0	2	0	0	1	0	0
G	3	0	15	0	0	0	1	0	0	0
T	1	0	2	22	0	11	7	13	0	22
	A	A	G	T	A	w	A	w	A	T

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8	9	10
A	22	0	13	7	11	0	22	2	0	1
C	0	0	0	1	0	0	0	15	0	3
G	0	0	1	0	0	2	0	1	0	0
T	0	22	8	14	11	20	0	4	22	18
	A	T	w	T	w	T	A	C	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
ENSMUSG00000070362	Target	Mus musculus	chr3:112,974,935-112,974,944	+	AAGTCAATAT	–	ATATTGACTT
ENSMUSG00000070362_CFAM	Orthologue	Canis familiaris	chrUn:46,712,626-46,712,635	–	AACTATTTAT	+	ATAAATAGTT
ENSMUSG00000070362_CHOF	Orthologue	Choloepus hoffmanni	ENSMUSG00000070362_CHOF:375-384	+	TAGTATAAAT	–	ATTTATACTA
ENSMUSG00000070362_CJAC	Orthologue	Callithrix jacchus	ENSMUSG00000070362_CJAC:156-165	–	AAGTAAATAT	+	ATATTTACTT
ENSMUSG00000070362_CPOR	Orthologue	Cavia porcellus	ENSMUSG00000070362_CPOR:74-83	–	AAGTCAATAT	+	ATATTGACTT
ENSMUSG00000070362_DNOV	Orthologue	Dasypus novemcinctus	scaffold_140518:3,090-3,099	+	AATTAAATAT	–	ATATTTAATT
ENSMUSG00000070362_ECAB	Orthologue	Equus caballus	ENSMUSG00000070362_ECAB:387-396	+	GAATATAAAT	–	ATTTATATTC
ENSMUSG00000070362_ETEL	Orthologue	Echinops telfairi	scaffold_200667:2,970-2,979	–	AAATATTTAT	+	ATAAATATTT
ENSMUSG00000070362_FRUB	Orthologue	Fugu rubripes	chrUn:224,060,644-224,060,653	+	AAGTAAAAAT	–	ATTTTTACTT
ENSMUSG00000070362_GGAL	Orthologue	Gallus gallus	chr8:11,424,903-11,424,912	–	AAGTAAAAAT	+	ATTTTTACTT
ENSMUSG00000070362_HSAP	Orthologue	Homo sapiens	chr1:104,005,018-104,005,027	+	AAGTATTTAT	–	ATAAATACTT
ENSMUSG00000070362_LAFR	Orthologue	Loxodonta africana	scaffold_61363:1,091-1,100	–	AAGTAATAAT	+	ATTATTACTT
ENSMUSG00000070362_MDOM	Orthologue	Monodelphis domestica	scaffold_0:14,539,892-14,539,901	–	AAATAAATAT	+	ATATTTATTT
ENSMUSG00000070362_MMUL	Orthologue	Macaca mulatta	SCAFFOLD812:37,505-37,514	–	AAGTAAATAT	+	ATATTTACTT
ENSMUSG00000070362_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_155133:12,207-12,216	–	AAGTAAATAT	+	ATATTTACTT
ENSMUSG00000070362_OGAR	Orthologue	Otolemur garnettii	ENSMUSG00000070362_OGAR:257-266	+	GAGTATAAAT	–	ATTTATACTC
ENSMUSG00000070362_PPYG	Orthologue	Pongo pygmaeus	ENSMUSG00000070362_PPYG:208-217	+	AAATATAAAT	–	ATTTATATTT
ENSMUSG00000070362_PTRO	Orthologue	Pan troglodytes	chr1:103,080,625-103,080,634	+	AAGTATTTAT	–	ATAAATACTT
ENSMUSG00000070362_SSCR	Orthologue	Sus scrofa	ENSMUSG00000070362_SSCR:108-117	+	AAGTATTTAT	–	ATAAATACTT
ENSMUSG00000070362_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000070362_TBEL:13-22	+	GATTATAAAT	–	ATTTATAATC
ENSMUSG00000070362_TNIG	Orthologue	Tetraodon nigroviridis	15_random:2,106,120-2,106,129	+	AAGTAAGTAT	–	ATACTTACTT
ENSMUSG00000070362_XTRO	Orthologue	Xenopus tropicalis	scaffold_466:404,564-404,573	+	AAGTATTCAT	–	ATGAATACTT

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