FILTERS:
pvalue:0.1
Motif craMmus33878
More information about this gene at Ensembl.org Go to UCSC
The contents of this page can be modified by changing your filter settings.
Currently, this page only shows information about a motif if it:
+ has a discovery p-value < 0.1
Filters based on species and motif discovery algorithms are not applied to the contents of this page.

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 craMmus33878
Discovery p-value 2.79E-03
Motif location chr2: 86,629,428-86,629,437 (+) (10 bp)
Search region location chr2: 86,627,573-86,629,647 (+) (2,075 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 20 species: Mus musculus, Bos taurus, Canis familiaris, Choloepus hoffmanni, Callithrix jacchus, Cavia porcellus, Dasypus novemcinctus, Danio rerio, Equus caballus, Echinops telfairi, Homo sapiens, Loxodonta africana, Myotis lucifugus, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, Pan troglodytes, Sorex araneus, Spermophilus tridecemlineatus, Tupaia belangeri
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 10 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (9 annot.): TEF(7.40E-06) ,    POU1F1(5.05E-05) ,    RSRFC4(5.39E-05) ,    HNF-3(8.62E-05) ,    RSRFC4(1.02E-04) ...
ORegAnno: (1 annot.): FoxA1(6.44E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence AAAkATArAT ATyTATmTTT
Position frequency matrix
1 2 3 4 5 6 7 8 9 10
A 19 12 20 0 14 0 18 12 20 0
C 0 0 0 0 2 0 0 0 0 0
G 0 4 0 11 0 0 2 8 0 0
T 1 4 0 9 4 20 0 0 0 20
A r A k A T A r A T
1 2 3 4 5 6 7 8 9 10
A 20 0 0 0 20 4 9 0 4 1
C 0 0 8 2 0 0 11 0 4 0
G 0 0 0 0 0 2 0 0 0 0
T 0 20 12 18 0 14 0 20 12 19
A T y T A T m T w T

In the table below, bases highlighted on the Target sequence will link to a single nucleotide polymoprhism in NCBI's dbSNP.

Site Sequence Stack
Ensembl gene ID Type Species Position Std (+)Sequence Std (-)Sequence
ENSMUSG00000047969 Target Mus musculus chr2:86,629,428-86,629,437 + ATATATAAAT – ATTTATATAT
ENSMUSG00000047969_BTAU Orthologue Bos taurus chr2:620,572-620,581 + AAAGATAAAT – ATTTATCTTT
ENSMUSG00000047969_CFAM Orthologue Canis familiaris chr18:42,796,026-42,796,035 – AAATCTAAAT + ATTTAGATTT
ENSMUSG00000047969_CHOF Orthologue Choloepus hoffmanni ENSMUSG00000047969_CHOF:209-218 – AGAGATAGAT + ATCTATCTCT
ENSMUSG00000047969_CJAC Orthologue Callithrix jacchus ENSMUSG00000047969_CJAC:22-31 – ATATTTGAAT + ATTCAAATAT
ENSMUSG00000047969_CPOR Orthologue Cavia porcellus ENSMUSG00000047969_CPOR:513-522 – AAAGATAGAT + ATCTATCTTT
ENSMUSG00000047969_DNOV Orthologue Dasypus novemcinctus scaffold_94210:6,102-6,111 + AAATTTAAAT – ATTTAAATTT
ENSMUSG00000047969_DRER Orthologue Danio rerio chr21:38,695,852-38,695,861 – AAATTTAAAT + ATTTAAATTT
ENSMUSG00000047969_ECAB Orthologue Equus caballus ENSMUSG00000047969_ECAB:507-516 – AAAGATAGAT + ATCTATCTTT
ENSMUSG00000047969_ETEL Orthologue Echinops telfairi scaffold_279988:48,594-48,603 + AAATATAAAT – ATTTATATTT
ENSMUSG00000047969_HSAP Orthologue Homo sapiens chr11:55,776,157-55,776,166 – ATAGATGAAT + ATTCATCTAT
ENSMUSG00000047969_LAFR Orthologue Loxodonta africana scaffold_3364:95,533-95,542 – ATAGATAAAT + ATTTATCTAT
ENSMUSG00000047969_MLUC Orthologue Myotis lucifugus ENSMUSG00000047969_MLUC:352-361 – AAATCTAAAT + ATTTAGATTT
ENSMUSG00000047969_MMUL Orthologue Macaca mulatta SCAFFOLD46343:29,489-29,498 + AGAGATAGAT – ATCTATCTCT
ENSMUSG00000047969_OCUN Orthologue Oryctolagus cuniculus scaffold_173848:6,619-6,628 + AGAGATAGAT – ATCTATCTCT
ENSMUSG00000047969_OGAR Orthologue Otolemur garnettii ENSMUSG00000047969_OGAR:40-49 – TAATATAAAT + ATTTATATTA
ENSMUSG00000047969_PTRO Orthologue Pan troglodytes chr9:56,630,980-56,630,989 – AGAGATAGAT + ATCTATCTCT
ENSMUSG00000047969_SARA Orthologue Sorex araneus ENSMUSG00000047969_SARA:390-399 – AAATTTAAAT + ATTTAAATTT
ENSMUSG00000047969_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000047969_STRI:269-278 – AAAGATAGAT + ATCTATCTTT
ENSMUSG00000047969_TBEL Orthologue Tupaia belangeri ENSMUSG00000047969_TBEL:335-344 – AAAGATAGAT + ATCTATCTTT

Questions or comments: cisred@bcgsc.ca