FILTERS:
pvalue:0.1
Motif craMmus396442
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 craMmus396442
Discovery p-value 2.79E-03
Motif location chr11: 96,390,947-96,390,958 (+) (12 bp)
Search region location chr11: 96,389,405-96,391,143 (+) (1,739 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 22 species: Mus musculus, Bos taurus, Canis familiaris, Cavia porcellus, Danio rerio, Equus caballus, Erinaceus europaeus, Echinops telfairi, Gallus gallus, Homo sapiens, Monodelphis domestica, Macropus eugenii, Macaca mulatta, Oryctolagus cuniculus, Procavia capensis, Pongo pygmaeus, Pan troglodytes, Rattus norvegicus, Sus scrofa, Spermophilus tridecemlineatus, Tupaia belangeri, Xenopus tropicalis
Found with
'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.): YY1(3.06E-04) ,    aMEF-2(3.89E-04) ,    MEF-2A(8.94E-04)
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
27 (CUTL1__YY1)     119 (Nkx6-2__YY1)     123 (Cdc5__aMEF-2)     137 (IRF-7A__aMEF-2)     151 (IPF1__aMEF-2)     215 (HNF-1alpha__YY1)     222 (POU6F1_(c2)__YY1)     292 (Cdx-2__aMEF-2)     312 (POU3F1__YY1)     317 (POU6F1_(c2)__aMEF-2)     390 (IRF-7A__YY1)     532 (Pax-6__YY1)     582 (Pax-6__aMEF-2)     739 (Elk-1__YY1)     767 (HNF-1alpha__aMEF-2)     776 (HNF-3__YY1)     787 (CUTL1__aMEF-2)     797 (Sox9__aMEF-2)     802 (POU3F1__aMEF-2)     817 (Nkx6-2__aMEF-2)     818 (YY1__c-Ets-1)     851 (POU2F1__aMEF-2)     890 (C-EBPalpha__aMEF-2)     911 (S8__YY1)     1056 (CAR__YY1)     1160 (YY1__aMEF-2)     1236 (HFH-1__aMEF-2)     1241 (IPF1__YY1)     1428 (HNF-3__aMEF-2)     1450 (S8__aMEF-2)     1504 (aMEF-2__aMEF-2)     1540 (CAR__aMEF-2)     1591 (POU2F1__YY1)     1595 (Egr-1__YY1)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence CTTTAAATATGA TCATATTTAAAG
Position frequency matrix
1 2 3 4 5 6 7 8 9 10 11 12
A 0 0 0 0 22 22 22 0 16 0 0 22
C 15 3 3 0 0 0 0 0 0 0 6 0
G 0 1 0 0 0 0 0 0 6 0 16 0
T 7 18 19 22 0 0 0 22 0 22 0 0
C T T T A A A T A T G A
1 2 3 4 5 6 7 8 9 10 11 12
A 0 0 22 0 22 0 0 0 22 19 18 7
C 0 16 0 6 0 0 0 0 0 0 1 0
G 0 6 0 0 0 0 0 0 0 3 3 15
T 22 0 0 16 0 22 22 22 0 0 0 0
T C A T A T T T A A A G

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
ENSMUSG00000056648 Target Mus musculus chr11:96,390,947-96,390,958 + CTTTAAATATGA – TCATATTTAAAG
ENSMUSG00000056648_BTAU Orthologue Bos taurus chr19:31,232,358-31,232,369 – CTTTAAATATGA + TCATATTTAAAG
ENSMUSG00000056648_CFAM Orthologue Canis familiaris chr9:28,205,247-28,205,258 – CCTTAAATATGA + TCATATTTAAGG
ENSMUSG00000056648_CPOR Orthologue Cavia porcellus ENSMUSG00000056648_CPOR:342-353 + CTTTAAATATGA – TCATATTTAAAG
ENSMUSG00000056648_DRER Orthologue Danio rerio chr23:49,497,705-49,497,716 – TTTTAAATGTCA + TGACATTTAAAA
ENSMUSG00000056648_ECAB Orthologue Equus caballus ENSMUSG00000056648_ECAB:54-65 + CTTTAAATATGA – TCATATTTAAAG
ENSMUSG00000056648_EEUR Orthologue Erinaceus europaeus ENSMUSG00000056648_EEUR:119-130 + CTTTAAATATGA – TCATATTTAAAG
ENSMUSG00000056648_ETEL Orthologue Echinops telfairi scaffold_316744:59,855-59,866 + CTTTAAATATGA – TCATATTTAAAG
ENSMUSG00000056648_GGAL Orthologue Gallus gallus chr27:2,226,854-2,226,865 – TTTTAAATGTCA + TGACATTTAAAA
ENSMUSG00000056648_HSAP Orthologue Homo sapiens chr17:44,048,101-44,048,112 – CTTTAAATATGA + TCATATTTAAAG
ENSMUSG00000056648_MDOM Orthologue Monodelphis domestica scaffold_18:45,581,307-45,581,318 + CCTTAAATATGA – TCATATTTAAGG
ENSMUSG00000056648_MEUG Orthologue Macropus eugenii ENSMUSG00000056648_MEUG:262-273 + CCTTAAATATGA – TCATATTTAAGG
ENSMUSG00000056648_MMUL Orthologue Macaca mulatta SCAFFOLD60055:57,687-57,698 – CTTTAAATATGA + TCATATTTAAAG
ENSMUSG00000056648_OCUN Orthologue Oryctolagus cuniculus scaffold_203826:148,306-148,317 – TTCTAAATGTCA + TGACATTTAGAA
ENSMUSG00000056648_PCAP Orthologue Procavia capensis ENSMUSG00000056648_PCAP:668-679 – TTCTAAATGTCA + TGACATTTAGAA
ENSMUSG00000056648_PPYG Orthologue Pongo pygmaeus ENSMUSG00000056648_PPYG:668-679 + CTTTAAATATGA – TCATATTTAAAG
ENSMUSG00000056648_PTRO Orthologue Pan troglodytes 19_random:42,997,081-42,997,092 – CTTTAAATATGA + TCATATTTAAAG
ENSMUSG00000056648_RNOR Orthologue Rattus norvegicus chr10:85,027,147-85,027,158 + CTTTAAATATGA – TCATATTTAAAG
ENSMUSG00000056648_SSCR Orthologue Sus scrofa ENSMUSG00000056648_SSCR:460-471 – TTTTAAATGTCA + TGACATTTAAAA
ENSMUSG00000056648_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000056648_STRI:557-568 – TTCTAAATGTCA + TGACATTTAGAA
ENSMUSG00000056648_TBEL Orthologue Tupaia belangeri ENSMUSG00000056648_TBEL:648-659 + CTTTAAATATGA – TCATATTTAAAG
ENSMUSG00000056648_XTRO Orthologue Xenopus tropicalis scaffold_329:584,745-584,756 – TGTTAAATATGA + TCATATTTAACA

Questions or comments: cisred@bcgsc.ca