cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000056648 > craMmus387239

Motif craMmus387239

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	craMmus387239
Discovery p-value	2.79E-03
Motif location	chr11: 96,389,575-96,389,584 (+) (10 bp)
Search region location	chr11: 96,389,405-96,391,143 (+) (1,739 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	22 species: Mus musculus, Bos taurus, Canis familiaris, Callithrix jacchus, Cavia porcellus, Equus caballus, Erinaceus europaeus, Echinops telfairi, Gallus gallus, Homo sapiens, Monodelphis domestica, Macropus eugenii, Macaca mulatta, Oryctolagus cuniculus, Procavia capensis, Pongo pygmaeus, Pan troglodytes, 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 5 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (5 annot.): C-EBPgamma(3.28E-04) , YY1(3.91E-04) , aMEF-2(6.14E-04) , MEF-2A(6.22E-04) , aMEF-2(9.29E-04) ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 29 (C-EBPgamma__HNF-1alpha) 80 (C-EBPgamma__Nkx6-2) 119 (Nkx6-2__YY1) 215 (HNF-1alpha__YY1) 305 (C-EBPgamma__Chx10) 570 (C-EBPgamma__IRF-1) 769 (FOXO1__YY1) 793 (IRF-1__YY1) 815 (Lhx3a__YY1) 826 (Chx10__YY1) 864 (C-EBPgamma__MEF-2A) 938 (C-EBPgamma__aMEF-2) 955 (AFP1__YY1) 978 (MEF-2A__YY1) 1160 (YY1__aMEF-2) 1375 (C-EBPgamma__Lhx3a) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

ATTTTTmCGA

TCGkAAAAAT

Position frequency matrix

	1	2	3	4	5	6	7	8	9	10
A	21	0	0	0	1	3	12	0	5	22
C	0	0	0	0	0	0	10	19	0	0
G	0	0	3	0	0	0	0	3	17	0
T	1	22	19	22	21	19	0	0	0	0
	A	T	T	T	T	T	m	C	G	A

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8	9	10
A	0	0	0	0	19	21	22	19	22	1
C	0	17	3	0	0	0	0	3	0	0
G	0	0	19	10	0	0	0	0	0	0
T	22	5	0	12	3	1	0	0	0	21
	T	C	G	k	A	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
ENSMUSG00000056648	Target	Mus musculus	chr11:96,389,575-96,389,584	+	ATTTTTACAA	–	TTGTAAAAAT
ENSMUSG00000056648_BTAU	Orthologue	Bos taurus	chr19:31,232,223-31,232,232	–	ATTTTTCCGA	+	TCGGAAAAAT
ENSMUSG00000056648_CFAM	Orthologue	Canis familiaris	chr9:28,206,705-28,206,714	–	ATTTTTACAA	+	TTGTAAAAAT
ENSMUSG00000056648_CJAC	Orthologue	Callithrix jacchus	ENSMUSG00000056648_CJAC:1,150-1,159	+	TTTTTAACGA	–	TCGTTAAAAA
ENSMUSG00000056648_CPOR	Orthologue	Cavia porcellus	ENSMUSG00000056648_CPOR:479-488	+	ATTTTTCCGA	–	TCGGAAAAAT
ENSMUSG00000056648_ECAB	Orthologue	Equus caballus	ENSMUSG00000056648_ECAB:192-201	+	ATTTTTCCGA	–	TCGGAAAAAT
ENSMUSG00000056648_EEUR	Orthologue	Erinaceus europaeus	ENSMUSG00000056648_EEUR:152-161	+	ATGTTTACGA	–	TCGTAAACAT
ENSMUSG00000056648_ETEL	Orthologue	Echinops telfairi	scaffold_316744:59,992-60,001	+	ATTTTTCCGA	–	TCGGAAAAAT
ENSMUSG00000056648_GGAL	Orthologue	Gallus gallus	chr27:2,226,880-2,226,889	–	ATTTTAACGA	+	TCGTTAAAAT
ENSMUSG00000056648_HSAP	Orthologue	Homo sapiens	chr17:44,049,539-44,049,548	–	ATTTTTACAA	+	TTGTAAAAAT
ENSMUSG00000056648_MDOM	Orthologue	Monodelphis domestica	scaffold_18:45,581,340-45,581,349	+	ATGTTTAGGA	–	TCCTAAACAT
ENSMUSG00000056648_MEUG	Orthologue	Macropus eugenii	ENSMUSG00000056648_MEUG:295-304	+	ATGTTTAGGA	–	TCCTAAACAT
ENSMUSG00000056648_MMUL	Orthologue	Macaca mulatta	SCAFFOLD60055:59,116-59,125	–	ATTTTTACAA	+	TTGTAAAAAT
ENSMUSG00000056648_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_203826:148,288-148,297	+	ATTTTTCCGA	–	TCGGAAAAAT
ENSMUSG00000056648_PCAP	Orthologue	Procavia capensis	ENSMUSG00000056648_PCAP:650-659	+	ATTTTTCCGA	–	TCGGAAAAAT
ENSMUSG00000056648_PPYG	Orthologue	Pongo pygmaeus	ENSMUSG00000056648_PPYG:807-816	+	ATTTTTCCGA	–	TCGGAAAAAT
ENSMUSG00000056648_PTRO	Orthologue	Pan troglodytes	19_random:42,998,518-42,998,527	–	ATTTTTACAA	+	TTGTAAAAAT
ENSMUSG00000056648_RNOR	Orthologue	Rattus norvegicus	chr10:85,027,284-85,027,293	+	ATTTTTCCGA	–	TCGGAAAAAT
ENSMUSG00000056648_SARA	Orthologue	Sorex araneus	ENSMUSG00000056648_SARA:468-477	–	ATTTTAACGA	+	TCGTTAAAAT
ENSMUSG00000056648_SSCR	Orthologue	Sus scrofa	ENSMUSG00000056648_SSCR:442-451	+	ATTTTTCCGA	–	TCGGAAAAAT
ENSMUSG00000056648_STRI	Orthologue	Spermophilus tridecemlineatus	ENSMUSG00000056648_STRI:539-548	+	ATTTTTCCGA	–	TCGGAAAAAT
ENSMUSG00000056648_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000056648_TBEL:736-745	+	ATTTATAGGA	–	TCCTATAAAT

Export Site Sequences Stack