cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000060176 > craMmus297905

Motif craMmus297905

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	craMmus297905
Discovery p-value	2.79E-03
Motif location	chr13: 57,449,389-57,449,398 (-) (10 bp)
Search region location	chr13: 57,449,337-57,452,126 (-) (2,790 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	22 species: Mus musculus, Canis familiaris, Choloepus hoffmanni, Cavia porcellus, Dasypus novemcinctus, Danio rerio, Equus caballus, Erinaceus europaeus, Gallus gallus, Loxodonta africana, Monodelphis domestica, Myotis lucifugus, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, Procavia capensis, Pongo pygmaeus, Rattus norvegicus, Sorex araneus, Sus scrofa, Spermophilus tridecemlineatus, Tupaia belangeri
Found with	MotifSampler
'De Novo' motif group ID	This motif was not submitted for clustering.
Similar to (annotation p-value)	There are 3 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (3 annot.): IRF-1(9.14E-05) , Pax-6(1.36E-04) , IRF-2(4.44E-04) ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 23 (HNF-1alpha__Pax-6) 201 (Nkx3-1__Pax-6) 363 (IRF-1__POU3F1) 412 (AFP1__IRF-1) 457 (IRF-1__Nkx6-2) 516 (E4BP4__IRF-1) 532 (Pax-6__YY1) 546 (AFP1__Pax-6) 772 (POU6F1_(c2)__Pax-6) 788 (POU3F1__Pax-6) 793 (IRF-1__YY1) 905 (IRF-1__Nkx3-1) 1043 (Chx10__Pax-6) 1084 (POU1F1__Pax-6) 1088 (Pax-6__TEF) 1171 (E4BP4__Pax-6) 1195 (IRF-1__TEF) 1207 (Chx10__IRF-1) 1285 (IRF-1__POU1F1) 1486 (Nkx6-2__Pax-6) 1514 (HNF-1alpha__IRF-1) 1599 (IRF-1__POU6F1_(c2)) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

CAAAATCAAA

TTTGATTTTG

Position frequency matrix

	1	2	3	4	5	6	7	8	9	10
A	1	20	22	22	22	2	3	21	22	22
C	19	0	0	0	0	0	19	0	0	0
G	0	2	0	0	0	0	0	0	0	0
T	2	0	0	0	0	20	0	1	0	0
	C	A	A	A	A	T	C	A	A	A

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8	9	10
A	0	0	1	0	20	0	0	0	0	2
C	0	0	0	0	0	0	0	0	2	0
G	0	0	0	19	0	0	0	0	0	19
T	22	22	21	3	2	22	22	22	20	1
	T	T	T	G	A	T	T	T	T	G

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
ENSMUSG00000060176	Target	Mus musculus	chr13:57,449,389-57,449,398	+	CAAAATCAAA	–	TTTGATTTTG
ENSMUSG00000060176_CFAM	Orthologue	Canis familiaris	chr1:78,614,751-78,614,760	–	CAAAATCAAA	+	TTTGATTTTG
ENSMUSG00000060176_CHOF	Orthologue	Choloepus hoffmanni	ENSMUSG00000060176_CHOF:272-281	–	CAAAATCAAA	+	TTTGATTTTG
ENSMUSG00000060176_CPOR	Orthologue	Cavia porcellus	ENSMUSG00000060176_CPOR:340-349	–	CAAAAACAAA	+	TTTGTTTTTG
ENSMUSG00000060176_DNOV	Orthologue	Dasypus novemcinctus	scaffold_152038:1,334-1,343	–	CAAAATCAAA	+	TTTGATTTTG
ENSMUSG00000060176_DRER	Orthologue	Danio rerio	chr7:6,017,504-6,017,513	+	TAAAAACTAA	–	TTAGTTTTTA
ENSMUSG00000060176_ECAB	Orthologue	Equus caballus	ENSMUSG00000060176_ECAB:492-501	–	CAAAATCAAA	+	TTTGATTTTG
ENSMUSG00000060176_EEUR	Orthologue	Erinaceus europaeus	ENSMUSG00000060176_EEUR:46-55	–	CAAAATAAAA	+	TTTTATTTTG
ENSMUSG00000060176_GGAL	Orthologue	Gallus gallus	Z_random:12,705,756-12,705,765	+	CGAAATCAAA	–	TTTGATTTCG
ENSMUSG00000060176_LAFR	Orthologue	Loxodonta africana	scaffold_6625:11,075-11,084	–	AAAAATCAAA	+	TTTGATTTTT
ENSMUSG00000060176_MDOM	Orthologue	Monodelphis domestica	scaffold_17:50,959,044-50,959,053	–	TGAAATCAAA	+	TTTGATTTCA
ENSMUSG00000060176_MLUC	Orthologue	Myotis lucifugus	ENSMUSG00000060176_MLUC:450-459	–	CAAAATCAAA	+	TTTGATTTTG
ENSMUSG00000060176_MMUL	Orthologue	Macaca mulatta	SCAFFOLD70912:22,853-22,862	+	CAAAATCAAA	–	TTTGATTTTG
ENSMUSG00000060176_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_150197:403-412	–	CAAAATCAAA	+	TTTGATTTTG
ENSMUSG00000060176_OGAR	Orthologue	Otolemur garnettii	ENSMUSG00000060176_OGAR:402-411	–	CAAAATCAAA	+	TTTGATTTTG
ENSMUSG00000060176_PCAP	Orthologue	Procavia capensis	ENSMUSG00000060176_PCAP:405-414	–	CAAAATAAAA	+	TTTTATTTTG
ENSMUSG00000060176_PPYG	Orthologue	Pongo pygmaeus	ENSMUSG00000060176_PPYG:610-619	–	CAAAATCAAA	+	TTTGATTTTG
ENSMUSG00000060176_RNOR	Orthologue	Rattus norvegicus	chr17:12,235,154-12,235,163	–	CAAAATAAAA	+	TTTTATTTTG
ENSMUSG00000060176_SARA	Orthologue	Sorex araneus	ENSMUSG00000060176_SARA:580-589	–	CAAAATCAAA	+	TTTGATTTTG
ENSMUSG00000060176_SSCR	Orthologue	Sus scrofa	ENSMUSG00000060176_SSCR:650-659	–	CAAAATCAAA	+	TTTGATTTTG
ENSMUSG00000060176_STRI	Orthologue	Spermophilus tridecemlineatus	ENSMUSG00000060176_STRI:632-641	–	CAAAATCAAA	+	TTTGATTTTG
ENSMUSG00000060176_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000060176_TBEL:500-509	–	CAAAATCAAA	+	TTTGATTTTG

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