cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000025255 > craMmus106407

Motif craMmus106407

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	craMmus106407
Discovery p-value	2.79E-03
Motif location	chr3: 5,223,239-5,223,246 (+) (8 bp)
Search region location	chr3: 5,222,724-5,224,580 (+) (1,857 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	22 species: Mus musculus, Bos taurus, Canis familiaris, Callithrix jacchus, Cavia porcellus, Echinops telfairi, Felis catus, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Myotis lucifugus, Macaca mulatta, Procavia capensis, Pongo pygmaeus, Pan troglodytes, Rattus norvegicus, Sorex araneus, Spermophilus tridecemlineatus, 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 5 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (5 annot.): Chx10(2.55E-05) , Cdx-2(9.78E-05) , S8(2.10E-04) , Nkx3-1(3.06E-04) , Evi-1(4.82E-04) ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 60 (Cdx-2__HNF-1alpha) 254 (Cdx-2__Chx10) 303 (Chx10__POU3F1) 536 (Chx10__HNF-1alpha) 678 (POU3F1__S8) 707 (Chx10__S8) 907 (S8__STAT5A) 940 (HNF-1alpha__Nkx3-1) 1010 (Chx10__Nkx3-1) 1112 (Lhx3a__S8) 1147 (HNF-1alpha__S8) 1274 (Nkx3-1__POU3F1) 1366 (Lhx3a__Nkx3-1) 1394 (Chx10__Chx10) 1409 (Cdx-2__Lhx3a) 1427 (Chx10__STAT5A) 1518 (Nkx3-1__STAT5A) 1520 (Cdx-2__POU3F1) 1551 (Cdx-2__STAT5A) 1552 (Chx10__Lhx3a) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

TAATTAGA

TCTAATTA

Position frequency matrix

	1	2	3	4	5	6	7	8
A	0	22	22	0	0	22	0	22
C	0	0	0	0	0	0	6	0
G	0	0	0	0	0	0	16	0
T	22	0	0	22	22	0	0	0
	T	A	A	T	T	A	G	A

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8
A	0	0	0	22	22	0	0	22
C	0	16	0	0	0	0	0	0
G	0	6	0	0	0	0	0	0
T	22	0	22	0	0	22	22	0
	T	C	T	A	A	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
ENSMUSG00000025255	Target	Mus musculus	chr3:5,223,239-5,223,246	+	TAATTAGA	–	TCTAATTA
ENSMUSG00000025255_BTAU	Orthologue	Bos taurus	chr28:18,887,600-18,887,607	–	TAATTAGA	+	TCTAATTA
ENSMUSG00000025255_CFAM	Orthologue	Canis familiaris	chr29:27,665,401-27,665,408	+	TAATTAGA	–	TCTAATTA
ENSMUSG00000025255_CJAC	Orthologue	Callithrix jacchus	ENSMUSG00000025255_CJAC:487-494	+	TAATTAGA	–	TCTAATTA
ENSMUSG00000025255_CPOR	Orthologue	Cavia porcellus	ENSMUSG00000025255_CPOR:526-533	+	TAATTAGA	–	TCTAATTA
ENSMUSG00000025255_ETEL	Orthologue	Echinops telfairi	scaffold_285937:708-715	+	TAATTACA	–	TGTAATTA
ENSMUSG00000025255_FCAT	Orthologue	Felis catus	ENSMUSG00000025255_FCAT:440-447	+	TAATTAGA	–	TCTAATTA
ENSMUSG00000025255_FRUB	Orthologue	Fugu rubripes	chrUn:142,148,707-142,148,714	–	TAATTACA	+	TGTAATTA
ENSMUSG00000025255_GGAL	Orthologue	Gallus gallus	chr2:118,793,991-118,793,998	+	TAATTAGA	–	TCTAATTA
ENSMUSG00000025255_HSAP	Orthologue	Homo sapiens	chr8:77,755,003-77,755,010	+	TAATTAGA	–	TCTAATTA
ENSMUSG00000025255_LAFR	Orthologue	Loxodonta africana	scaffold_620:159,440-159,447	+	TAATTAGA	–	TCTAATTA
ENSMUSG00000025255_MLUC	Orthologue	Myotis lucifugus	ENSMUSG00000025255_MLUC:225-232	+	TAATTAGA	–	TCTAATTA
ENSMUSG00000025255_MMUL	Orthologue	Macaca mulatta	SCAFFOLD80045:253,111-253,118	–	TAATTAGA	+	TCTAATTA
ENSMUSG00000025255_PCAP	Orthologue	Procavia capensis	ENSMUSG00000025255_PCAP:260-267	+	TAATTACA	–	TGTAATTA
ENSMUSG00000025255_PPYG	Orthologue	Pongo pygmaeus	ENSMUSG00000025255_PPYG:250-257	+	TAATTACA	–	TGTAATTA
ENSMUSG00000025255_PTRO	Orthologue	Pan troglodytes	chr7:79,829,661-79,829,668	+	TAATTAGA	–	TCTAATTA
ENSMUSG00000025255_RNOR	Orthologue	Rattus norvegicus	chr2:98,680,853-98,680,860	–	TAATTAGA	+	TCTAATTA
ENSMUSG00000025255_SARA	Orthologue	Sorex araneus	ENSMUSG00000025255_SARA:240-247	+	TAATTAGA	–	TCTAATTA
ENSMUSG00000025255_STRI	Orthologue	Spermophilus tridecemlineatus	ENSMUSG00000025255_STRI:531-538	+	TAATTAGA	–	TCTAATTA
ENSMUSG00000025255_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000025255_TBEL:526-533	+	TAATTAGA	–	TCTAATTA
ENSMUSG00000025255_TNIG	Orthologue	Tetraodon nigroviridis	chr6:615,236-615,243	+	TAATTACA	–	TGTAATTA
ENSMUSG00000025255_XTRO	Orthologue	Xenopus tropicalis	scaffold_663:670,242-670,249	+	TAATTACA	–	TGTAATTA

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