FILTERS:
pvalue:0.1
Motif craMmus221206
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 craMmus221206
Discovery p-value 2.79E-03
Motif location chr2: 86,670,985-86,670,994 (+) (10 bp)
Search region location chr2: 86,670,834-86,672,669 (+) (1,836 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 15 species: Mus musculus, Canis familiaris, Choloepus hoffmanni, Dasypus novemcinctus, Danio rerio, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, 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.): POU2F1(1.19E-06) ,    POU3F2(1.37E-04) ,    POU3F2(2.06E-04) ,    POU3F1(2.75E-04) ,    POU6F1_(c2)(2.85E-04) ...
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
46 (HNF-3__POU6F1_(c2))     136 (HNF-6__POU3F1)     236 (POU6F1_(c2)__Pbx1a)     252 (POU3F2__POU3F2)     256 (POU3F1__Pbx1a)     274 (IPF1__POU2F1)     301 (IPF1__POU3F1)     317 (POU6F1_(c2)__aMEF-2)     340 (Cdx-2__POU3F2)     359 (MRF-2__POU3F2)     366 (HNF-3__POU3F1)     375 (HNF-3__POU2F1)     399 (POU3F2__aMEF-2)     468 (HNF-6__POU6F1_(c2))     488 (HNF-6__POU3F2)     501 (MRF-2__POU6F1_(c2))     569 (POU2F1__Pbx1a)     636 (IPF1__POU3F2)     709 (IPF1__POU6F1_(c2))     755 (POU3F1__POU3F2)     759 (HNF-6__POU2F1)     766 (POU3F2__Pbx1a)     802 (POU3F1__aMEF-2)     851 (POU2F1__aMEF-2)     858 (HNF-3__POU3F2)     916 (Cdx-2__POU2F1)     979 (HOXA3__POU2F1)     998 (POU2F1__POU3F2)     1336 (POU3F2__POU6F1_(c2))     1373 (HOXA3__POU3F2)     1410 (Cdx-2__POU6F1_(c2))     1448 (MRF-2__POU2F1)     1520 (Cdx-2__POU3F1)     1571 (MRF-2__POU3F1)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence ATATTTTAAw sTTAAAATAT
Position frequency matrix
1 2 3 4 5 6 7 8 9 10
A 15 0 15 0 3 0 4 10 14 8
C 0 0 0 0 0 0 0 4 1 0
G 0 0 0 0 0 0 0 1 0 0
T 0 15 0 15 12 15 11 0 0 7
A T A T T T T A A w
1 2 3 4 5 6 7 8 9 10
A 7 0 0 11 15 12 15 0 15 0
C 0 0 1 0 0 0 0 0 0 0
G 0 1 4 0 0 0 0 0 0 0
T 8 14 10 4 0 3 0 15 0 15
w T T A A A A T 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
ENSMUSG00000044213 Target Mus musculus chr2:86,670,985-86,670,994 + ATATTTTAAT – ATTAAAATAT
ENSMUSG00000044213_CFAM Orthologue Canis familiaris chr18:42,795,592-42,795,601 + ATATTTTAAA – TTTAAAATAT
ENSMUSG00000044213_CHOF Orthologue Choloepus hoffmanni ENSMUSG00000044213_CHOF:55-64 + ATATTTAAAA – TTTTAAATAT
ENSMUSG00000044213_DNOV Orthologue Dasypus novemcinctus scaffold_4603:23,494-23,503 – ATATTTTAAT + ATTAAAATAT
ENSMUSG00000044213_DRER Orthologue Danio rerio chr15:35,871,282-35,871,291 + ATATTTTCAA – TTGAAAATAT
ENSMUSG00000044213_GGAL Orthologue Gallus gallus chr5:57,783-57,792 – ATATATTCAT + ATGAATATAT
ENSMUSG00000044213_HSAP Orthologue Homo sapiens chr11:55,798,306-55,798,315 – ATATTTAAAT + ATTTAAATAT
ENSMUSG00000044213_LAFR Orthologue Loxodonta africana scaffold_806:104,343-104,352 – ATATTTTAAT + ATTAAAATAT
ENSMUSG00000044213_MDOM Orthologue Monodelphis domestica scaffold_33:20,999,610-20,999,619 + ATATATTGAA – TTCAATATAT
ENSMUSG00000044213_MMUL Orthologue Macaca mulatta SCAFFOLD46343:29,960-29,969 + ATATTTAAAA – TTTTAAATAT
ENSMUSG00000044213_OCUN Orthologue Oryctolagus cuniculus scaffold_173848:43,532-43,541 – ATATTTTAAA + TTTAAAATAT
ENSMUSG00000044213_OGAR Orthologue Otolemur garnettii ENSMUSG00000044213_OGAR:286-295 – ATATTTTCCA + TGGAAAATAT
ENSMUSG00000044213_PTRO Orthologue Pan troglodytes chr9:56,646,974-56,646,983 – ATATTTAAAT + ATTTAAATAT
ENSMUSG00000044213_RNOR Orthologue Rattus norvegicus chr3:69,863,407-69,863,416 + ATATTTTAAA – TTTAAAATAT
ENSMUSG00000044213_XTRO Orthologue Xenopus tropicalis scaffold_10:3,516,733-3,516,742 – ATATATTCAT + ATGAATATAT

Questions or comments: cisred@bcgsc.ca