cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000063804 > craMmus429413

Motif craMmus429413

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	craMmus429413
Discovery p-value	2.79E-03
Motif location	chr10: 45,281,874-45,281,885 (-) (12 bp)
Search region location	chr10: 45,281,817-45,283,516 (-) (1,700 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	21 species: Mus musculus, Canis familiaris, Callithrix jacchus, Cavia porcellus, Dasypus novemcinctus, Equus caballus, Erinaceus europaeus, Echinops telfairi, Felis catus, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Otolemur garnettii, Procavia capensis, 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 4 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (4 annot.): YY1(1.16E-04) , C-EBPbeta(8.22E-04) , ER-alpha(9.23E-04) , RFX1(9.71E-04) ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 119 (Nkx6-2__YY1) 140 (Evi-1__YY1) 222 (POU6F1_(c2)__YY1) 330 (CTF__YY1) 397 (C-EBPgamma__YY1) 793 (IRF-1__YY1) 826 (Chx10__YY1) 911 (S8__YY1) 937 (FOXP1a__YY1) 1096 (FOXJ2__YY1) 1158 (COUP__YY1) 1182 (AIRE__YY1) 1479 (E12__YY1) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

ATGTTGCCCCAC

GTGGGGCAACAT

Position frequency matrix

	1	2	3	4	5	6	7	8	9	10	11	12
A	15	0	0	0	0	0	0	0	0	4	20	0
C	0	0	0	1	0	5	20	21	21	17	1	16
G	0	0	20	0	0	16	1	0	0	0	0	5
T	6	21	1	20	21	0	0	0	0	0	0	0
	A	T	G	T	T	G	C	C	C	C	A	C

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8	9	10	11	12
A	0	0	0	0	0	0	0	21	20	1	21	6
C	5	0	0	0	0	1	16	0	0	20	0	0
G	16	1	17	21	21	20	5	0	1	0	0	0
T	0	20	4	0	0	0	0	0	0	0	0	15
	G	T	G	G	G	G	C	A	A	C	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
ENSMUSG00000063804	Target	Mus musculus	chr10:45,281,874-45,281,885	+	ATGTTGCCCCAC	–	GTGGGGCAACAT
ENSMUSG00000063804_CFAM	Orthologue	Canis familiaris	chr12:65,412,973-65,412,984	–	ATGTTGCCCCAC	+	GTGGGGCAACAT
ENSMUSG00000063804_CJAC	Orthologue	Callithrix jacchus	ENSMUSG00000063804_CJAC:91-102	–	TTGTTCCCCAAG	+	CTTGGGGAACAA
ENSMUSG00000063804_CPOR	Orthologue	Cavia porcellus	ENSMUSG00000063804_CPOR:382-393	–	ATGTTGCCCCAC	+	GTGGGGCAACAT
ENSMUSG00000063804_DNOV	Orthologue	Dasypus novemcinctus	scaffold_11741:10,519-10,530	–	ATGTTGCCCCAC	+	GTGGGGCAACAT
ENSMUSG00000063804_ECAB	Orthologue	Equus caballus	ENSMUSG00000063804_ECAB:1,659-1,670	–	ATGTTGCCCCAC	+	GTGGGGCAACAT
ENSMUSG00000063804_EEUR	Orthologue	Erinaceus europaeus	ENSMUSG00000063804_EEUR:226-237	–	TTTCTGGCCCCC	+	GGGGGCCAGAAA
ENSMUSG00000063804_ETEL	Orthologue	Echinops telfairi	scaffold_311644:1,347-1,358	+	ATGTTGCCCCAC	–	GTGGGGCAACAT
ENSMUSG00000063804_FCAT	Orthologue	Felis catus	ENSMUSG00000063804_FCAT:314-325	–	ATGTTGCCCCAC	+	GTGGGGCAACAT
ENSMUSG00000063804_GGAL	Orthologue	Gallus gallus	chr3:67,357,054-67,357,065	+	ATGTTGCCCCAC	–	GTGGGGCAACAT
ENSMUSG00000063804_HSAP	Orthologue	Homo sapiens	chr6:105,510,835-105,510,846	–	TTGTTCCCCAAG	+	CTTGGGGAACAA
ENSMUSG00000063804_LAFR	Orthologue	Loxodonta africana	scaffold_41030:9,372-9,383	–	TTGTTCCCCAAG	+	CTTGGGGAACAA
ENSMUSG00000063804_MDOM	Orthologue	Monodelphis domestica	scaffold_0:116,778,360-116,778,371	+	ATGTTGCCCCAC	–	GTGGGGCAACAT
ENSMUSG00000063804_MMUL	Orthologue	Macaca mulatta	SCAFFOLD35340:9,560-9,571	–	ATGTTGCCCCAC	+	GTGGGGCAACAT
ENSMUSG00000063804_OGAR	Orthologue	Otolemur garnettii	ENSMUSG00000063804_OGAR:593-604	–	TTGTTCCCCCAG	+	CTGGGGGAACAA
ENSMUSG00000063804_PCAP	Orthologue	Procavia capensis	ENSMUSG00000063804_PCAP:589-600	–	TTGTTCCCCAAG	+	CTTGGGGAACAA
ENSMUSG00000063804_RNOR	Orthologue	Rattus norvegicus	chr20:49,794,663-49,794,674	+	ATGTTGCCCCAC	–	GTGGGGCAACAT
ENSMUSG00000063804_SARA	Orthologue	Sorex araneus	ENSMUSG00000063804_SARA:1,543-1,554	–	ATGTTGCCCCAC	+	GTGGGGCAACAT
ENSMUSG00000063804_SSCR	Orthologue	Sus scrofa	ENSMUSG00000063804_SSCR:402-413	–	ATGTTGCCCCAC	+	GTGGGGCAACAT
ENSMUSG00000063804_STRI	Orthologue	Spermophilus tridecemlineatus	ENSMUSG00000063804_STRI:1,106-1,117	–	ATGTTGCCCCAC	+	GTGGGGCAACAT
ENSMUSG00000063804_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000063804_TBEL:1,596-1,607	–	ATGTTGCCCCAC	+	GTGGGGCAACAT

Export Site Sequences Stack