cisRED: cis-regulatory element database

cisRED > Mouse 3.1 > gene. ENSMUSG00000059873 > craMmus295735

Motif craMmus295735

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	craMmus295735
Discovery p-value	2.79E-03
Motif location	chr2: 85,818,428-85,818,435 (+) (8 bp)
Search region location	chr2: 85,817,461-85,819,160 (+) (1,700 bp)
Assembly	Mouse, Ensembl v38 (NCBI m35)
Found in	23 species: Mus musculus, Bos taurus, Canis familiaris, Choloepus hoffmanni, Callithrix jacchus, Cavia porcellus, Dasypus novemcinctus, Equus caballus, Erinaceus europaeus, Echinops telfairi, Felis catus, Homo sapiens, Monodelphis domestica, Myotis lucifugus, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, Procavia capensis, Pan troglodytes, Rattus norvegicus, Sorex araneus, 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 6 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (6 annot.): Pax-6(9.62E-05) , Nkx3-1(1.58E-04) , RSRFC4(3.31E-04) , POU3F2(4.87E-04) , HNF-1alpha(5.56E-04) ... ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	Annotation-based: 23 (HNF-1alpha__Pax-6) 84 (Nkx3-1__TEF) 201 (Nkx3-1__Pax-6) 203 (CUTL1__Nkx3-1) 219 (HNF-1alpha__RSRFC4) 271 (CUTL1__RSRFC4) 280 (COMP1__RSRFC4) 293 (Pax-6__RSRFC4) 546 (AFP1__Pax-6) 598 (Pax-6__Pax-6) 627 (AFP1__RSRFC4) 777 (RSRFC4__TEF) 781 (COMP1__Nkx3-1) 921 (CUTL1__Pax-6) 927 (Nkx3-1__POU1F1) 940 (HNF-1alpha__Nkx3-1) 976 (Nkx3-1__Pbx1a) 987 (Brachyury__RSRFC4) 1029 (Pbx1a__RSRFC4) 1059 (AFP1__Nkx3-1) 1084 (POU1F1__Pax-6) 1088 (Pax-6__TEF) 1093 (Pax-6__Pbx1a) 1199 (Brachyury__Pax-6) 1361 (COMP1__Pax-6) 1363 (POU1F1__RSRFC4) No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

ATGTACTT

AAGTACAT

Position frequency matrix

	1	2	3	4	5	6	7	8
A	19	0	3	0	23	0	1	0
C	0	0	0	0	0	22	1	0
G	0	0	19	0	0	0	0	0
T	4	23	1	23	0	1	21	23
	A	T	G	T	A	C	T	T

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7	8
A	23	21	1	0	23	1	23	4
C	0	0	0	0	0	19	0	0
G	0	1	22	0	0	0	0	0
T	0	1	0	23	0	3	0	19
	A	A	G	T	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
ENSMUSG00000059873	Target	Mus musculus	chr2:85,818,428-85,818,435	+	TTATACTT	–	AAGTATAA
ENSMUSG00000059873_BTAU	Orthologue	Bos taurus	chr1:22,265,312-22,265,319	+	ATGTATTT	–	AAATACAT
ENSMUSG00000059873_CFAM	Orthologue	Canis familiaris	chr18:42,488,299-42,488,306	+	ATGTACTT	–	AAGTACAT
ENSMUSG00000059873_CHOF	Orthologue	Choloepus hoffmanni	ENSMUSG00000059873_CHOF:245-252	+	ATGTACTT	–	AAGTACAT
ENSMUSG00000059873_CJAC	Orthologue	Callithrix jacchus	ENSMUSG00000059873_CJAC:190-197	+	TTTTACTT	–	AAGTAAAA
ENSMUSG00000059873_CPOR	Orthologue	Cavia porcellus	ENSMUSG00000059873_CPOR:986-993	+	ATGTACTT	–	AAGTACAT
ENSMUSG00000059873_DNOV	Orthologue	Dasypus novemcinctus	scaffold_51051:7,945-7,952	–	ATGTACTT	+	AAGTACAT
ENSMUSG00000059873_ECAB	Orthologue	Equus caballus	ENSMUSG00000059873_ECAB:118-125	–	TTGTACTT	+	AAGTACAA
ENSMUSG00000059873_EEUR	Orthologue	Erinaceus europaeus	ENSMUSG00000059873_EEUR:497-504	+	ATGTACTT	–	AAGTACAT
ENSMUSG00000059873_ETEL	Orthologue	Echinops telfairi	scaffold_286042:41,798-41,805	–	ATGTACAT	+	ATGTACAT
ENSMUSG00000059873_FCAT	Orthologue	Felis catus	ENSMUSG00000059873_FCAT:473-480	+	ATGTACCT	–	AGGTACAT
ENSMUSG00000059873_HSAP	Orthologue	Homo sapiens	chr11:56,067,839-56,067,846	–	ATATACTT	+	AAGTATAT
ENSMUSG00000059873_MDOM	Orthologue	Monodelphis domestica	scaffold_33:19,257,025-19,257,032	–	ATGTACTT	+	AAGTACAT
ENSMUSG00000059873_MLUC	Orthologue	Myotis lucifugus	ENSMUSG00000059873_MLUC:36-43	–	TTATACTT	+	AAGTATAA
ENSMUSG00000059873_MMUL	Orthologue	Macaca mulatta	SCAFFOLD31127:4,865-4,872	+	ATGTACTT	–	AAGTACAT
ENSMUSG00000059873_OCUN	Orthologue	Oryctolagus cuniculus	scaffold_165671:4,350-4,357	–	ATGTACTT	+	AAGTACAT
ENSMUSG00000059873_OGAR	Orthologue	Otolemur garnettii	ENSMUSG00000059873_OGAR:1,661-1,668	+	ATGTACTT	–	AAGTACAT
ENSMUSG00000059873_PCAP	Orthologue	Procavia capensis	ENSMUSG00000059873_PCAP:409-416	+	ATGTACTT	–	AAGTACAT
ENSMUSG00000059873_PTRO	Orthologue	Pan troglodytes	chr9:56,749,112-56,749,119	+	ATGTACTT	–	AAGTACAT
ENSMUSG00000059873_RNOR	Orthologue	Rattus norvegicus	chr3:69,084,105-69,084,112	+	ATGTACTT	–	AAGTACAT
ENSMUSG00000059873_SARA	Orthologue	Sorex araneus	ENSMUSG00000059873_SARA:457-464	+	ATGTACTT	–	AAGTACAT
ENSMUSG00000059873_STRI	Orthologue	Spermophilus tridecemlineatus	ENSMUSG00000059873_STRI:443-450	+	ATGTACTT	–	AAGTACAT
ENSMUSG00000059873_TBEL	Orthologue	Tupaia belangeri	ENSMUSG00000059873_TBEL:454-461	+	ATGTACTT	–	AAGTACAT

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