cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000053129 > craMmus367384

Motif craMmus367384

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	craMmus367384
Discovery p-value	2.79E-03
Motif location	chr5: 146,082,962-146,082,967 (+) (6 bp)
Search region location	chr5: 146,081,600-146,083,299 (+) (1,700 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	22 species: Mus musculus, Bos taurus, Canis familiaris, Callithrix jacchus, Danio rerio, Equus caballus, Erinaceus europaeus, Fugu rubripes, Homo sapiens, Monodelphis domestica, Macropus eugenii, Myotis lucifugus, Macaca mulatta, Ornithorhynchus anatinus, Procavia capensis, Pan troglodytes, Rattus norvegicus, Sorex araneus, Sus scrofa, Tupaia belangeri, Tetraodon nigroviridis, Xenopus tropicalis
Found with	MotifSampler
'De Novo' motif group ID	This motif was not submitted for clustering.
Similar to (annotation p-value)	There are 7 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (7 annot.): HOXA5(8.98E-06) , AhR(3.04E-04) , HIF-1(3.37E-04) , MTF-1(3.83E-04) , AhR(4.97E-04) ... ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 204 (HOXA5__HOXA5) 489 (AhR__CAR) 599 (AhR__AhR) 700 (AFP1__HOXA5) 873 (CAR__HOXA5) 896 (AhR__MTF-1) 904 (HOXA5__IPF1) 1062 (HNF-1alpha__HOXA5) 1225 (AhR__YY1) 1227 (AhR__HIF-1) 1356 (HOXA5__IRF-1) 1367 (HIF-1__YY1) 1439 (Evi-1__HOXA5) 1477 (HES-1__HIF-1) 1519 (AhR__HES-1) 1525 (HOXA5__YY1) 1544 (MTF-1__YY1) 1583 (HOXA5__POU3F1) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

AGCGTG

CACGCT

Position frequency matrix

	1	2	3	4	5	6
A	22	0	0	0	0	0
C	0	0	22	0	0	0
G	0	22	0	22	0	22
T	0	0	0	0	22	0
	A	G	C	G	T	G

Transfac

Jaspar

CSV

	1	2	3	4	5	6
A	0	22	0	0	0	0
C	22	0	22	0	22	0
G	0	0	0	22	0	0
T	0	0	0	0	0	22
	C	A	C	G	C	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
ENSMUSG00000053129	Target	Mus musculus	chr5:146,082,962-146,082,967	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_BTAU	Orthologue	Bos taurus	chr12:17,058,525-17,058,530	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_CFAM	Orthologue	Canis familiaris	chr25:14,843,068-14,843,073	–	AGCGTG	+	CACGCT
ENSMUSG00000053129_CJAC	Orthologue	Callithrix jacchus	ENSMUSG00000053129_CJAC:689-694	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_DRER	Orthologue	Danio rerio	chr7:54,100,707-54,100,712	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_ECAB	Orthologue	Equus caballus	ENSMUSG00000053129_ECAB:1,160-1,165	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_EEUR	Orthologue	Erinaceus europaeus	ENSMUSG00000053129_EEUR:1,134-1,139	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_FRUB	Orthologue	Fugu rubripes	chrUn:4,735,751-4,735,756	–	AGCGTG	+	CACGCT
ENSMUSG00000053129_HSAP	Orthologue	Homo sapiens	chr13:27,264,496-27,264,501	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_MDOM	Orthologue	Monodelphis domestica	scaffold_15:36,959,824-36,959,829	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_MEUG	Orthologue	Macropus eugenii	ENSMUSG00000053129_MEUG:379-384	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_MLUC	Orthologue	Myotis lucifugus	ENSMUSG00000053129_MLUC:568-573	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_MMUL	Orthologue	Macaca mulatta	SCAFFOLD5087:70,515-70,520	–	AGCGTG	+	CACGCT
ENSMUSG00000053129_OANA	Orthologue	Ornithorhynchus anatinus	ENSMUSG00000053129_OANA:165-170	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_PCAP	Orthologue	Procavia capensis	ENSMUSG00000053129_PCAP:1,156-1,161	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_PTRO	Orthologue	Pan troglodytes	chr14:26,450,432-26,450,437	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_RNOR	Orthologue	Rattus norvegicus	chr12:8,580,746-8,580,751	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_SARA	Orthologue	Sorex araneus	ENSMUSG00000053129_SARA:163-168	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_SSCR	Orthologue	Sus scrofa	ENSMUSG00000053129_SSCR:531-536	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000053129_TBEL:1,190-1,195	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_TNIG	Orthologue	Tetraodon nigroviridis	chr7:4,250,756-4,250,761	+	AGCGTG	–	CACGCT
ENSMUSG00000053129_XTRO	Orthologue	Xenopus tropicalis	scaffold_449:557,963-557,968	+	AGCGTG	–	CACGCT

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