cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000058251 > craMmus293404

Motif craMmus293404

More information about this gene at Ensembl.org

The contents of this page can be modified by changing your filter settings.
Currently, this page only shows information about a motif if it:
+ has a discovery p-value < 0.1
Filters based on species and motif discovery algorithms are not applied to the contents of this page.

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	craMmus293404
Discovery p-value	2.79E-03
Motif location	chr10: 129,583,484-129,583,493 (+) (10 bp)
Search region location	chr10: 129,582,852-129,585,178 (+) (2,327 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	18 species: Mus musculus, Bos taurus, Canis familiaris, Choloepus hoffmanni, Dasypus novemcinctus, Danio rerio, Echinops telfairi, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Otolemur garnettii, Pongo pygmaeus, Pan troglodytes, Tupaia belangeri, Tetraodon nigroviridis
Found with	MotifSampler
'De Novo' motif group ID	This motif was not submitted for clustering.
Similar to (annotation p-value)	There are 12 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (11 annot.): AIRE(1.16E-04) , HNF-1alpha(1.70E-04) , HNF-1alpha(1.85E-04) , RSRFC4(2.36E-04) , TEF(2.38E-04) ... ORegAnno: (1 annot.): FoxA1(4.25E-04)
Modules (Co-occurring motif patterns)	Annotation-based: 8 (Nkx6-2__STAT5A) 79 (Nkx6-2__POU3F2) 116 (AIRE__STAT5A) 185 (HNF-1alpha__HNF-3) 188 (AIRE__Evi-1) 350 (AIRE__HNF-3) 379 (Evi-1__HNF-1alpha) 446 (Evi-1__RSRFC4) 632 (HNF-3__Nkx6-2) 647 (RSRFC4__STAT5A) 698 (HNF-1alpha__HTF) 729 (HNF-3__RSRFC4) 820 (Evi-1__TEF) 944 (POU3F2__RSRFC4) 965 (HNF-1alpha__STAT5A) 1167 (POU3F2__TEF) 1185 (AIRE__POU3F2) 1307 (Evi-1__Nkx6-2) 1414 (AIRE__HTF) 1476 (HNF-1alpha__POU3F2) 1565 (HNF-3__TEF) 1588 (STAT5A__TEF) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

ATATTTAynT

AnrTAAATAT

Position frequency matrix

	1	2	3	4	5	6	7	8	9	10
A	16	0	15	2	0	0	17	0	8	0
C	0	0	0	2	0	4	1	8	5	0
G	0	0	0	0	0	1	0	0	0	0
T	2	18	3	14	18	13	0	10	5	18
	A	T	A	T	T	T	A	y	n	T

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8	9	10
A	18	5	10	0	13	18	14	3	18	2
C	0	0	0	0	1	0	0	0	0	0
G	0	5	8	1	4	0	2	0	0	0
T	0	8	0	17	0	0	2	15	0	16
	A	n	r	T	A	A	A	T	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
ENSMUSG00000058251	Target	Mus musculus	chr10:129,583,484-129,583,493	+	ATATTTATTT	–	AAATAAATAT
ENSMUSG00000058251_BTAU	Orthologue	Bos taurus	chr5:35,272,931-35,272,940	+	ATTTTTATCT	–	AGATAAAAAT
ENSMUSG00000058251_CFAM	Orthologue	Canis familiaris	chr27:3,069,976-3,069,985	+	ATATTTATTT	–	AAATAAATAT
ENSMUSG00000058251_CHOF	Orthologue	Choloepus hoffmanni	ENSMUSG00000058251_CHOF:420-429	+	TTATTTATCT	–	AGATAAATAA
ENSMUSG00000058251_DNOV	Orthologue	Dasypus novemcinctus	scaffold_21905:4,654-4,663	–	ATATTTATAT	+	ATATAAATAT
ENSMUSG00000058251_DRER	Orthologue	Danio rerio	chr15:35,919,231-35,919,240	+	ATATTTATAT	–	ATATAAATAT
ENSMUSG00000058251_ETEL	Orthologue	Echinops telfairi	scaffold_303156:40,060-40,069	–	ATACTTACTT	+	AAGTAAGTAT
ENSMUSG00000058251_FRUB	Orthologue	Fugu rubripes	chrUn:265,469,850-265,469,859	+	ATATTTACAT	–	ATGTAAATAT
ENSMUSG00000058251_GGAL	Orthologue	Gallus gallus	chr5:83,216-83,225	+	ATAATCACTT	–	AAGTGATTAT
ENSMUSG00000058251_HSAP	Orthologue	Homo sapiens	chr12:53,942,738-53,942,747	+	ATATTCACCT	–	AGGTGAATAT
ENSMUSG00000058251_LAFR	Orthologue	Loxodonta africana	scaffold_5385:49,482-49,491	–	ATTTTTACAT	+	ATGTAAAAAT
ENSMUSG00000058251_MDOM	Orthologue	Monodelphis domestica	scaffold_33:19,531,362-19,531,371	+	ATATTCATAT	–	ATATGAATAT
ENSMUSG00000058251_MMUL	Orthologue	Macaca mulatta	SCAFFOLD15668:26,396-26,405	+	ATATTTATAT	–	ATATAAATAT
ENSMUSG00000058251_OGAR	Orthologue	Otolemur garnettii	ENSMUSG00000058251_OGAR:438-447	+	ATACTCATCT	–	AGATGAGTAT
ENSMUSG00000058251_PPYG	Orthologue	Pongo pygmaeus	ENSMUSG00000058251_PPYG:401-410	–	ATAATTATCT	+	AGATAATTAT
ENSMUSG00000058251_PTRO	Orthologue	Pan troglodytes	chr10:55,199,354-55,199,363	+	ATATTGACAT	–	ATGTCAATAT
ENSMUSG00000058251_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000058251_TBEL:591-600	+	ATTTTTCCTT	–	AAGGAAAAAT
ENSMUSG00000058251_TNIG	Orthologue	Tetraodon nigroviridis	chr2:14,366,253-14,366,262	–	TTATTTACAT	+	ATGTAAATAA

Export Site Sequences Stack