FILTERS:
pvalue:0.1
Motif craMmus395884
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 craMmus395884
Discovery p-value 2.79E-03
Motif location chr11: 96,390,933-96,390,947 (+) (15 bp)
Search region location chr11: 96,389,405-96,391,143 (+) (1,739 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 21 species: Mus musculus, Bos taurus, Canis familiaris, Callithrix jacchus, Cavia porcellus, Echinops telfairi, Felis catus, Homo sapiens, Monodelphis domestica, Macropus eugenii, Myotis lucifugus, Macaca mulatta, Oryctolagus cuniculus, Procavia capensis, Pongo pygmaeus, Pan troglodytes, Rattus norvegicus, Sorex araneus, Sus scrofa, 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 3 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (3 annot.): Nkx6-2(9.66E-05) ,    IPF1(1.97E-04) ,    YY1(4.52E-04)
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
34 (Nkx6-2__Nkx6-2)     38 (Nkx6-2__POU6F1_(c2))     119 (Nkx6-2__YY1)     127 (HFH-1__Nkx6-2)     151 (IPF1__aMEF-2)     199 (IPF1__S8)     228 (IPF1__IPF1)     274 (IPF1__POU2F1)     301 (IPF1__POU3F1)     387 (CUTL1__IPF1)     419 (IPF1__Pax-6)     422 (Cdc5__Nkx6-2)     433 (Nkx6-2__POU2F1)     602 (HNF-1alpha__Nkx6-2)     632 (HNF-3__Nkx6-2)     652 (Cdc5__IPF1)     709 (IPF1__POU6F1_(c2))     783 (Nkx6-2__Sox9)     790 (CAR__Nkx6-2)     817 (Nkx6-2__aMEF-2)     856 (Cdx-2__IPF1)     953 (IPF1__Nkx6-2)     1000 (HNF-1alpha__IPF1)     1013 (Nkx6-2__S8)     1241 (IPF1__YY1)     1255 (Cdx-2__Nkx6-2)     1283 (Nkx6-2__POU3F1)     1316 (IRF-7A__Nkx6-2)     1358 (CUTL1__Nkx6-2)     1426 (HNF-3__IPF1)     1454 (IPF1__Sox9)     1465 (IPF1__IRF-7A)     1486 (Nkx6-2__Pax-6)     1594 (CAR__IPF1)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence AywGmkCATwAAAGC GCTTTsATGmkCsrT
Position frequency matrix
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
A 14 1 9 1 12 0 0 21 0 8 21 21 21 0 0
C 0 8 0 0 8 0 21 0 0 0 0 0 0 0 21
G 7 0 0 20 1 9 0 0 0 0 0 0 0 21 0
T 0 12 12 0 0 12 0 0 21 13 0 0 0 0 0
A y w G m k C A T n A A A G C
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
A 0 0 0 0 0 13 21 0 0 12 0 0 12 12 0
C 0 21 0 0 0 0 0 0 0 9 1 20 0 0 7
G 21 0 0 0 0 0 0 0 21 0 8 0 0 8 0
T 0 0 21 21 21 8 0 21 0 0 12 1 9 1 14
G C T T T n A T G m k C w r 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
ENSMUSG00000056648 Target Mus musculus chr11:96,390,933-96,390,947 + ATTGATCATTAAAGC – GCTTTAATGATCAAT
ENSMUSG00000056648_BTAU Orthologue Bos taurus chr19:31,232,369-31,232,383 – ATTGATCATTAAAGC + GCTTTAATGATCAAT
ENSMUSG00000056648_CFAM Orthologue Canis familiaris chr9:28,205,258-28,205,272 – ATTGATCATTAAAGC + GCTTTAATGATCAAT
ENSMUSG00000056648_CJAC Orthologue Callithrix jacchus ENSMUSG00000056648_CJAC:1,583-1,597 + ATTGATCATTAAAGC – GCTTTAATGATCAAT
ENSMUSG00000056648_CPOR Orthologue Cavia porcellus ENSMUSG00000056648_CPOR:328-342 + ATTGATCATTAAAGC – GCTTTAATGATCAAT
ENSMUSG00000056648_ETEL Orthologue Echinops telfairi scaffold_316744:59,841-59,855 + ATTGATCATTAAAGC – GCTTTAATGATCAAT
ENSMUSG00000056648_FCAT Orthologue Felis catus ENSMUSG00000056648_FCAT:343-357 – GCAGCGCATAAAAGC + GCTTTTATGCGCTGC
ENSMUSG00000056648_HSAP Orthologue Homo sapiens chr17:44,048,112-44,048,126 – ATTGATCATTAAAGC + GCTTTAATGATCAAT
ENSMUSG00000056648_MDOM Orthologue Monodelphis domestica scaffold_18:45,581,143-45,581,157 – ACAGCGCATAAAAGC + GCTTTTATGCGCTGT
ENSMUSG00000056648_MEUG Orthologue Macropus eugenii ENSMUSG00000056648_MEUG:96-110 – ACAGCGCATAAAAGC + GCTTTTATGCGCTGT
ENSMUSG00000056648_MLUC Orthologue Myotis lucifugus ENSMUSG00000056648_MLUC:496-510 – GCAGCGCATAAAAGC + GCTTTTATGCGCTGC
ENSMUSG00000056648_MMUL Orthologue Macaca mulatta SCAFFOLD60055:57,698-57,712 – ATTGATCATTAAAGC + GCTTTAATGATCAAT
ENSMUSG00000056648_OCUN Orthologue Oryctolagus cuniculus scaffold_203826:148,137-148,151 + ATTGATCATTAAAGC – GCTTTAATGATCAAT
ENSMUSG00000056648_PCAP Orthologue Procavia capensis ENSMUSG00000056648_PCAP:341-355 – GCAGCGCATAAAAGC + GCTTTTATGCGCTGC
ENSMUSG00000056648_PPYG Orthologue Pongo pygmaeus ENSMUSG00000056648_PPYG:654-668 + ATTGATCATTAAAGC – GCTTTAATGATCAAT
ENSMUSG00000056648_PTRO Orthologue Pan troglodytes 19_random:42,997,092-42,997,106 – ATTGATCATTAAAGC + GCTTTAATGATCAAT
ENSMUSG00000056648_RNOR Orthologue Rattus norvegicus chr10:85,027,133-85,027,147 + ATTGATCATTAAAGC – GCTTTAATGATCAAT
ENSMUSG00000056648_SARA Orthologue Sorex araneus ENSMUSG00000056648_SARA:158-172 – GAAAGGCATTAAAGC + GCTTTAATGCCTTTC
ENSMUSG00000056648_SSCR Orthologue Sus scrofa ENSMUSG00000056648_SSCR:142-156 – GCAGCGCATAAAAGC + GCTTTTATGCGCTGC
ENSMUSG00000056648_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000056648_STRI:235-249 – GCAGCGCATAAAAGC + GCTTTTATGCGCTGC
ENSMUSG00000056648_TBEL Orthologue Tupaia belangeri ENSMUSG00000056648_TBEL:485-499 – GCAGCGCATAAAAGC + GCTTTTATGCGCTGC

Questions or comments: cisred@bcgsc.ca