FILTERS:
pvalue:0.1
Motif craMmus10027
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 craMmus10027
Discovery p-value 2.79E-03
Motif location chr12: 36,615,256-36,615,267 (+) (12 bp)
Search region location chr12: 36,613,710-36,615,409 (+) (1,700 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 22 species: Mus musculus, Canis familiaris, Callithrix jacchus, Cavia porcellus, Dasypus novemcinctus, Equus caballus, Erinaceus europaeus, Echinops telfairi, Felis catus, Gallus gallus, Homo sapiens, Loxodonta africana, Myotis lucifugus, Macaca mulatta, 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 9 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (8 annot.): POU6F1_(c2)(7.06E-05) ,    Lhx3a(8.01E-05) ,    S8(2.10E-04) ,    HOXA5(3.04E-04) ,    HNF-1alpha(5.89E-04) ...
ORegAnno: (1 annot.): FoxA1(9.28E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
25 (FOXJ2__Lhx3a)     31 (CUTL1__POU6F1_(c2))     112 (CUTL1__S8)     180 (CUTL1__HOXA5)     221 (OCA-B__S8)     236 (POU6F1_(c2)__Pbx1a)     438 (HOXA5__POU2F1)     463 (Evi-1__Lhx3a)     464 (Evi-1__S8)     475 (CAR__Lhx3a)     519 (Evi-1__POU6F1_(c2))     654 (COMP1__HOXA5)     658 (CUTL1__Lhx3a)     688 (Pbx1a__S8)     699 (HOXA5__SRF)     819 (OCA-B__POU6F1_(c2))     873 (CAR__HOXA5)     942 (POU2F1__POU6F1_(c2))     972 (Lhx3a__Pbx1a)     977 (HOXA5__Pbx1a)     1016 (FOXJ2__POU6F1_(c2))     1071 (COMP1__S8)     1079 (FOXJ2__HOXA5)     1129 (HOXA5__Pbx)     1181 (POU2F1__S8)     1183 (FOXJ2__S8)     1211 (Lhx3a__OCA-B)     1214 (CAR__S8)     1230 (COMP1__POU6F1_(c2))     1277 (COMP1__Lhx3a)     1309 (HOXA5__OCA-B)     1439 (Evi-1__HOXA5)     1445 (Lhx3a__POU2F1)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence ATAATTAATGTT AACATTAATTAT
Position frequency matrix
1 2 3 4 5 6 7 8 9 10 11 12
A 20 0 22 22 0 0 21 22 0 0 1 0
C 0 1 0 0 0 0 0 0 0 0 0 0
G 2 0 0 0 0 0 1 0 0 21 1 1
T 0 21 0 0 22 22 0 0 22 1 20 21
A T A A T T A A T G T T
1 2 3 4 5 6 7 8 9 10 11 12
A 21 20 1 22 0 0 22 22 0 0 21 0
C 1 1 21 0 0 1 0 0 0 0 0 2
G 0 0 0 0 0 0 0 0 0 0 1 0
T 0 1 0 0 22 21 0 0 22 22 0 20
A A C A T T A A T 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
ENSMUSG00000004151 Target Mus musculus chr12:36,615,256-36,615,267 + ATAATTAATGTT – AACATTAATTAT
ENSMUSG00000004151_CFAM Orthologue Canis familiaris chr14:31,709,155-31,709,166 – ATAATTGATGTT + AACATCAATTAT
ENSMUSG00000004151_CJAC Orthologue Callithrix jacchus ENSMUSG00000004151_CJAC:309-320 + GCAATTAATTAT – ATAATTAATTGC
ENSMUSG00000004151_CPOR Orthologue Cavia porcellus ENSMUSG00000004151_CPOR:494-505 + ATAATTAATGTT – AACATTAATTAT
ENSMUSG00000004151_DNOV Orthologue Dasypus novemcinctus scaffold_1550:49,053-49,064 + ATAATTAATGGT – ACCATTAATTAT
ENSMUSG00000004151_ECAB Orthologue Equus caballus ENSMUSG00000004151_ECAB:435-446 + ATAATTAATGTT – AACATTAATTAT
ENSMUSG00000004151_EEUR Orthologue Erinaceus europaeus ENSMUSG00000004151_EEUR:1,246-1,257 + GTAATTAATGTT – AACATTAATTAC
ENSMUSG00000004151_ETEL Orthologue Echinops telfairi scaffold_319874:47,293-47,304 – ATAATTAATGTT + AACATTAATTAT
ENSMUSG00000004151_FCAT Orthologue Felis catus ENSMUSG00000004151_FCAT:1,286-1,297 + ATAATTAATGTT – AACATTAATTAT
ENSMUSG00000004151_GGAL Orthologue Gallus gallus chr2:26,632,122-26,632,133 – ATAATTAATGTT + AACATTAATTAT
ENSMUSG00000004151_HSAP Orthologue Homo sapiens chr7:13,802,482-13,802,493 – ATAATTAATGTT + AACATTAATTAT
ENSMUSG00000004151_LAFR Orthologue Loxodonta africana scaffold_1790:71,318-71,329 – ATAATTAATGTT + AACATTAATTAT
ENSMUSG00000004151_MLUC Orthologue Myotis lucifugus ENSMUSG00000004151_MLUC:1,326-1,337 + ATAATTAATGTT – AACATTAATTAT
ENSMUSG00000004151_MMUL Orthologue Macaca mulatta SCAFFOLD71186:40,863-40,874 + ATAATTAATGTT – AACATTAATTAT
ENSMUSG00000004151_PCAP Orthologue Procavia capensis ENSMUSG00000004151_PCAP:482-493 + ATAATTAATGTT – AACATTAATTAT
ENSMUSG00000004151_PPYG Orthologue Pongo pygmaeus ENSMUSG00000004151_PPYG:1,596-1,607 + ATAATTAATGTT – AACATTAATTAT
ENSMUSG00000004151_PTRO Orthologue Pan troglodytes chr6:14,677,629-14,677,640 – ATAATTAATGTT + AACATTAATTAT
ENSMUSG00000004151_RNOR Orthologue Rattus norvegicus chr6:57,678,678-57,678,689 + ATAATTAATGTT – AACATTAATTAT
ENSMUSG00000004151_SARA Orthologue Sorex araneus ENSMUSG00000004151_SARA:1,569-1,580 + ATAATTAATGTT – AACATTAATTAT
ENSMUSG00000004151_SSCR Orthologue Sus scrofa ENSMUSG00000004151_SSCR:1,012-1,023 + ATAATTAATGTG – CACATTAATTAT
ENSMUSG00000004151_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000004151_STRI:1,344-1,355 + ATAATTAATGTT – AACATTAATTAT
ENSMUSG00000004151_TBEL Orthologue Tupaia belangeri ENSMUSG00000004151_TBEL:924-935 + ATAATTAATGTT – AACATTAATTAT

Questions or comments: cisred@bcgsc.ca