FILTERS:
pvalue:0.1
Motif craMmus181705
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 craMmus181705
Discovery p-value 2.79E-03
Motif location chr2: 87,739,098-87,739,105 (+) (8 bp)
Search region location chr2: 87,738,345-87,740,092 (+) (1,748 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 14 species: Mus musculus, Canis familiaris, Dasypus novemcinctus, Danio rerio, Equus caballus, Echinops telfairi, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Pan troglodytes, Rattus norvegicus, Xenopus tropicalis
Found with
'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.): POU3F2(5.20E-05) ,    S8(2.10E-04) ,    MEF-2A(6.02E-04) ,    aMEF-2(6.14E-04) ,    Chx10(7.37E-04) ...
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
43 (MEF-2A__POU3F2)     56 (POU3F2__Sox9)     79 (Nkx6-2__POU3F2)     96 (HNF-3__S8)     112 (CUTL1__S8)     160 (POU1F1__POU3F2)     199 (IPF1__S8)     221 (OCA-B__S8)     281 (Nkx3-1__S8)     340 (Cdx-2__POU3F2)     343 (POU1F1__S8)     362 (OCA-B__POU3F2)     391 (CUTL1__POU3F2)     399 (POU3F2__aMEF-2)     476 (E4BP4__POU3F2)     484 (Nkx2-2__POU3F2)     636 (IPF1__POU3F2)     678 (POU3F1__S8)     707 (Chx10__S8)     728 (HNF-3alpha__POU3F2)     755 (POU3F1__POU3F2)     764 (Cdx-2__S8)     833 (S8__Sox9)     858 (HNF-3__POU3F2)     919 (Nkx3-1__POU3F2)     944 (POU3F2__RSRFC4)     998 (POU2F1__POU3F2)     1013 (Nkx6-2__S8)     1048 (E4BP4__S8)     1112 (Lhx3a__S8)     1167 (POU3F2__TEF)     1177 (POU6F1_(c2)__S8)     1181 (POU2F1__S8)     1216 (S8__TEF)     1299 (Hlf__S8)     1336 (POU3F2__POU6F1_(c2))     1382 (Hlf__POU3F2)     1442 (Chx10__POU3F2)     1450 (S8__aMEF-2)     1452 (RSRFC4__S8)     1589 (Lhx3a__POU3F2)     1601 (MEF-2A__S8)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence wTAwAAAT ATTTsTAs
Position frequency matrix
1 2 3 4 5 6 7 8
A 8 0 14 7 14 14 14 0
C 0 0 0 3 0 0 0 0
G 0 0 0 0 0 0 0 0
T 6 14 0 4 0 0 0 14
w T A w A A A T
1 2 3 4 5 6 7 8
A 14 0 0 0 4 0 14 6
C 0 0 0 0 0 0 0 0
G 0 0 0 0 3 0 0 0
T 0 14 14 14 7 14 0 8
A T T T w T A w

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
ENSMUSG00000048197 Target Mus musculus chr2:87,739,098-87,739,105 + TTAAAAAT – ATTTTTAA
ENSMUSG00000048197_CFAM Orthologue Canis familiaris chr18:43,099,870-43,099,877 + ATAAAAAT – ATTTTTAT
ENSMUSG00000048197_DNOV Orthologue Dasypus novemcinctus scaffold_18954:4,723-4,730 + TTACAAAT – ATTTGTAA
ENSMUSG00000048197_DRER Orthologue Danio rerio chr15:36,007,003-36,007,010 + ATACAAAT – ATTTGTAT
ENSMUSG00000048197_ECAB Orthologue Equus caballus ENSMUSG00000048197_ECAB:52-59 + TTAAAAAT – ATTTTTAA
ENSMUSG00000048197_ETEL Orthologue Echinops telfairi scaffold_293493:198,853-198,860 + TTAAAAAT – ATTTTTAA
ENSMUSG00000048197_HSAP Orthologue Homo sapiens chr11:55,439,700-55,439,707 + ATATAAAT – ATTTATAT
ENSMUSG00000048197_LAFR Orthologue Loxodonta africana scaffold_3668:116,742-116,749 + ATAAAAAT – ATTTTTAT
ENSMUSG00000048197_MDOM Orthologue Monodelphis domestica scaffold_33:16,653,023-16,653,030 + ATAAAAAT – ATTTTTAT
ENSMUSG00000048197_MMUL Orthologue Macaca mulatta SCAFFOLD115116:156,151-156,158 – TTACAAAT + ATTTGTAA
ENSMUSG00000048197_OCUN Orthologue Oryctolagus cuniculus scaffold_173414:67,054-67,061 – ATATAAAT + ATTTATAT
ENSMUSG00000048197_PTRO Orthologue Pan troglodytes 9_random:27,082,621-27,082,628 + ATATAAAT – ATTTATAT
ENSMUSG00000048197_RNOR Orthologue Rattus norvegicus chr3:71,578,134-71,578,141 + TTAAAAAT – ATTTTTAA
ENSMUSG00000048197_XTRO Orthologue Xenopus tropicalis scaffold_10:4,101,456-4,101,463 + ATATAAAT – ATTTATAT

Questions or comments: cisred@bcgsc.ca