FILTERS:
pvalue:0.1
Motif craMmus398039
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 craMmus398039
Discovery p-value 2.79E-03
Motif location chr2: 87,299,556-87,299,565 (+) (10 bp)
Search region location chr2: 87,299,301-87,301,082 (+) (1,782 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 17 species: Mus musculus, Bos taurus, Canis familiaris, Choloepus hoffmanni, Dasypus novemcinctus, Danio rerio, Erinaceus europaeus, Echinops telfairi, Fugu rubripes, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macropus eugenii, Oryctolagus cuniculus, Rattus norvegicus, Sorex araneus, Tetraodon nigroviridis
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 5 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (5 annot.): IRF-1(1.64E-04) ,    IRF-7A(1.74E-04) ,    IRF-1(1.89E-04) ,    HNF-1alpha(3.59E-04) ,    IRF-1(8.71E-04)
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
50 (HNF-1alpha__HNF-6)     60 (Cdx-2__HNF-1alpha)     98 (Cdx-2__IRF-1)     152 (HNF-1alpha__IRF-7A)     191 (C-EBPbeta__HNF-1alpha)     210 (FOXJ2__HNF-1alpha)     268 (FOXJ2__IRF-7A)     354 (HNF-1alpha__factor_delta)     363 (IRF-1__POU3F1)     379 (Evi-1__HNF-1alpha)     536 (Chx10__HNF-1alpha)     555 (HNF-6__IRF-1)     590 (IRF-7A__POU1F1)     784 (IRF-7A__POU3F1)     813 (IRF-7A__Pbx1a)     844 (HNF-1alpha__Msx-1)     874 (FOXJ2__IRF-1)     929 (Evi-1__IRF-7A)     956 (Chx10__IRF-7A)     1023 (Cdx-2__IRF-7A)     1053 (Evi-1__IRF-1)     1124 (IRF-1__Pbx1a)     1197 (HNF-1alpha__Sox5)     1201 (IRF-7A__POU3F2)     1207 (Chx10__IRF-1)     1254 (HNF-1alpha__HNF-1alpha)     1285 (IRF-1__POU1F1)     1379 (HNF-1alpha__Pbx1a)     1476 (HNF-1alpha__POU3F2)     1482 (IRF-1__IRF-7A)     1492 (HNF-1alpha__POU3F1)     1514 (HNF-1alpha__IRF-1)     1532 (HNF-1alpha__HNF-3alpha)     1553 (C-EBPbeta__IRF-1)     1578 (IRF-1__POU3F2)     1600 (HNF-1alpha__POU1F1)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence ATTwyTATTT AAATArsAAT
Position frequency matrix
1 2 3 4 5 6 7 8 9 10
A 11 0 2 11 0 0 11 0 1 1
C 1 0 0 0 7 0 1 0 0 0
G 5 0 0 0 0 0 5 0 0 0
T 0 17 15 6 10 17 0 17 16 16
A T T n y T A T T T
1 2 3 4 5 6 7 8 9 10
A 16 16 17 0 17 10 6 15 17 0
C 0 0 0 5 0 0 0 0 0 5
G 0 0 0 1 0 7 0 0 0 1
T 1 1 0 11 0 0 11 2 0 11
A A A T A r n A A 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
ENSMUSG00000058194 Target Mus musculus chr2:87,299,556-87,299,565 + ATTTCTATTT – AAATAGAAAT
ENSMUSG00000058194_BTAU Orthologue Bos taurus chr2:605,744-605,753 + ATTATTGTTT – AAACAATAAT
ENSMUSG00000058194_CFAM Orthologue Canis familiaris chr18:43,005,049-43,005,058 + GTTTCTATTT – AAATAGAAAC
ENSMUSG00000058194_CHOF Orthologue Choloepus hoffmanni ENSMUSG00000058194_CHOF:222-231 + CTTATTGTTA – TAACAATAAG
ENSMUSG00000058194_DNOV Orthologue Dasypus novemcinctus scaffold_90506:5,436-5,445 + ATTATTGTTT – AAACAATAAT
ENSMUSG00000058194_DRER Orthologue Danio rerio chr21:14,186,305-14,186,314 – ATAATTATTT + AAATAATTAT
ENSMUSG00000058194_EEUR Orthologue Erinaceus europaeus ENSMUSG00000058194_EEUR:108-117 + GTTACTGTTT – AAACAGTAAC
ENSMUSG00000058194_ETEL Orthologue Echinops telfairi scaffold_240389:10,376-10,385 – ATTACTATAT + ATATAGTAAT
ENSMUSG00000058194_FRUB Orthologue Fugu rubripes chrUn:294,180,647-294,180,656 – ATTTTTATTT + AAATAAAAAT
ENSMUSG00000058194_HSAP Orthologue Homo sapiens chr11:55,493,188-55,493,197 – ATTACTATTT + AAATAGTAAT
ENSMUSG00000058194_LAFR Orthologue Loxodonta africana scaffold_144:35,833-35,842 – GTTTCTATTT + AAATAGAAAC
ENSMUSG00000058194_MDOM Orthologue Monodelphis domestica scaffold_33:17,379,406-17,379,415 – ATTATTATTT + AAATAATAAT
ENSMUSG00000058194_MEUG Orthologue Macropus eugenii ENSMUSG00000058194_MEUG:424-433 + ATTTTTCTTT – AAAGAAAAAT
ENSMUSG00000058194_OCUN Orthologue Oryctolagus cuniculus scaffold_110707:14,778-14,787 – GTTTCTGTTT + AAACAGAAAC
ENSMUSG00000058194_RNOR Orthologue Rattus norvegicus chr3:71,034,529-71,034,538 – ATTATTATTT + AAATAATAAT
ENSMUSG00000058194_SARA Orthologue Sorex araneus ENSMUSG00000058194_SARA:516-525 + ATTATTATTT – AAATAATAAT
ENSMUSG00000058194_TNIG Orthologue Tetraodon nigroviridis Un_random:126,487,386-126,487,395 + GTAATTATTT – AAATAATTAC

Questions or comments: cisred@bcgsc.ca