cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000070352 > craMmus389225

Motif craMmus389225

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	craMmus389225
Discovery p-value	2.79E-03
Motif location	chr3: 127,382,729-127,382,734 (-) (6 bp)
Search region location	chr3: 127,381,888-127,383,587 (-) (1,700 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	25 species: Mus musculus, Bos taurus, Canis familiaris, Callithrix jacchus, Dasypus novemcinctus, Equus caballus, Erinaceus europaeus, Echinops telfairi, Felis catus, Gallus gallus, Homo sapiens, Monodelphis domestica, Macropus eugenii, Myotis lucifugus, Macaca mulatta, Ornithorhynchus anatinus, Oryctolagus cuniculus, Otolemur garnettii, Procavia capensis, Pongo pygmaeus, Pan troglodytes, Sorex araneus, Spermophilus tridecemlineatus, Tupaia belangeri, Xenopus tropicalis
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.): Sox9(1.32E-04) , COMP1(2.77E-04) , CAR(5.38E-04) ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 48 (COMP1__Nkx2-1) 54 (COMP1__LEF-1) 56 (POU3F2__Sox9) 57 (OCA-B__Sox9) 62 (COMP1__CUTL1) 145 (COMP1__POU3F2) 216 (COMP1__aMEF-2) 294 (SRY__Sox9) 326 (STAT5A__Sox9) 434 (COMP1__POU2F1) 624 (COMP1__Nkx6-2) 656 (COMP1__OCA-B) 674 (COMP1__MEF-2A) 783 (Nkx6-2__Sox9) 797 (Sox9__aMEF-2) 835 (POU2F1__Sox9) 857 (COMP1__STAT5A) 1070 (AR__COMP1) 1310 (COMP1__HMG_I) 1335 (MEF-2A__Sox9) 1359 (CUTL1__Sox9) 1361 (COMP1__Pax-6) 1556 (COMP1__SRY) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

TAACAT

ATGTTA

Position frequency matrix

	1	2	3	4	5	6
A	7	25	25	0	25	0
C	0	0	0	25	0	0
G	0	0	0	0	0	0
T	18	0	0	0	0	25
	T	A	A	C	A	T

Transfac

Jaspar

CSV

	1	2	3	4	5	6
A	25	0	0	0	0	18
C	0	0	0	0	0	0
G	0	0	25	0	0	0
T	0	25	0	25	25	7
	A	T	G	T	T	A

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
ENSMUSG00000070352	Target	Mus musculus	chr3:127,382,729-127,382,734	+	TAACAT	–	ATGTTA
ENSMUSG00000070352_BTAU	Orthologue	Bos taurus	chr6:4,972,014-4,972,019	+	AAACAT	–	ATGTTT
ENSMUSG00000070352_CFAM	Orthologue	Canis familiaris	chr32:35,353,863-35,353,868	+	AAACAT	–	ATGTTT
ENSMUSG00000070352_CJAC	Orthologue	Callithrix jacchus	ENSMUSG00000070352_CJAC:604-609	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_DNOV	Orthologue	Dasypus novemcinctus	scaffold_15856:19,980-19,985	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_ECAB	Orthologue	Equus caballus	ENSMUSG00000070352_ECAB:227-232	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_EEUR	Orthologue	Erinaceus europaeus	ENSMUSG00000070352_EEUR:1,154-1,159	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_ETEL	Orthologue	Echinops telfairi	scaffold_313081:81,240-81,245	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_FCAT	Orthologue	Felis catus	ENSMUSG00000070352_FCAT:1,137-1,142	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_GGAL	Orthologue	Gallus gallus	chr4:57,612,399-57,612,404	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_HSAP	Orthologue	Homo sapiens	chr4:113,926,772-113,926,777	+	AAACAT	–	ATGTTT
ENSMUSG00000070352_MDOM	Orthologue	Monodelphis domestica	scaffold_9:81,365,635-81,365,640	+	TAACAT	–	ATGTTA
ENSMUSG00000070352_MEUG	Orthologue	Macropus eugenii	ENSMUSG00000070352_MEUG:174-179	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_MLUC	Orthologue	Myotis lucifugus	ENSMUSG00000070352_MLUC:826-831	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_MMUL	Orthologue	Macaca mulatta	SCAFFOLD126206:375-380	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_OANA	Orthologue	Ornithorhynchus anatinus	ENSMUSG00000070352_OANA:27-32	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_147322:3,295-3,300	+	TAACAT	–	ATGTTA
ENSMUSG00000070352_OGAR	Orthologue	Otolemur garnettii	ENSMUSG00000070352_OGAR:1,146-1,151	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_PCAP	Orthologue	Procavia capensis	ENSMUSG00000070352_PCAP:57-62	+	AAACAT	–	ATGTTT
ENSMUSG00000070352_PPYG	Orthologue	Pongo pygmaeus	ENSMUSG00000070352_PPYG:597-602	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_PTRO	Orthologue	Pan troglodytes	chr3:130,506,442-130,506,447	+	AAACAT	–	ATGTTT
ENSMUSG00000070352_SARA	Orthologue	Sorex araneus	ENSMUSG00000070352_SARA:700-705	+	AAACAT	–	ATGTTT
ENSMUSG00000070352_STRI	Orthologue	Spermophilus tridecemlineatus	ENSMUSG00000070352_STRI:427-432	–	TAACAT	+	ATGTTA
ENSMUSG00000070352_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000070352_TBEL:144-149	+	AAACAT	–	ATGTTT
ENSMUSG00000070352_XTRO	Orthologue	Xenopus tropicalis	scaffold_445:639,693-639,698	–	TAACAT	+	ATGTTA

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