FILTERS:
pvalue:0.1
Motif craMmus266225
More information about this gene at Ensembl.org Go to UCSC
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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 craMmus266225
Discovery p-value 2.79E-03
Motif location chr10: 129,413,715-129,413,720 (-) (6 bp)
Search region location chr10: 129,413,094-129,415,329 (-) (2,236 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 16 species: Mus musculus, Canis familiaris, Dasypus novemcinctus, Danio rerio, Erinaceus europaeus, Echinops telfairi, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Procavia capensis, Pan troglodytes, Spermophilus tridecemlineatus, Xenopus tropicalis
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 10 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (10 annot.): Chx10(2.23E-05) ,    Nkx2-5(1.07E-04) ,    Brachyury(1.17E-04) ,    IPF1(1.33E-04) ,    POU3F1(3.95E-04) ...
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
11 (Nkx2-5__RSRFC4)     24 (Brachyury__MEF-2A)     28 (Nkx2-5__POU3F2)     67 (Evi-1__POU3F1)     118 (Chx10__Evi-1)     177 (Brachyury__POU3F2)     231 (IPF1__IRF-1)     265 (Chx10__MEF-2A)     313 (FOXJ2__Nkx2-5)     328 (Brachyury__CUTL1)     329 (CUTL1__Chx10)     363 (IRF-1__POU3F1)     371 (Brachyury__HNF-1alpha)     383 (Brachyury__Evi-1)     384 (Chx10__FOXJ2)     387 (CUTL1__IPF1)     396 (FOXJ2__IPF1)     419 (IPF1__Pax-6)     536 (Chx10__HNF-1alpha)     636 (IPF1__POU3F2)     755 (POU3F1__POU3F2)     784 (IRF-7A__POU3F1)     788 (POU3F1__Pax-6)     836 (CUTL1__POU3F1)     845 (IPF1__MEF-2A)     876 (HNF-1alpha__Nkx2-5)     917 (FOXJ2__POU3F1)     953 (IPF1__Nkx6-2)     956 (Chx10__IRF-7A)     987 (Brachyury__RSRFC4)     1000 (HNF-1alpha__IPF1)     1024 (Brachyury__IRF-1)     1038 (IPF1__RSRFC4)     1043 (Chx10__Pax-6)     1097 (Nkx2-5__Nkx6-2)     1142 (Brachyury__Nkx6-2)     1199 (Brachyury__Pax-6)     1207 (Chx10__IRF-1)     1221 (Evi-1__IPF1)     1235 (MEF-2A__POU3F1)     1283 (Nkx6-2__POU3F1)     1429 (Chx10__RSRFC4)     1442 (Chx10__POU3F2)     1465 (IPF1__IRF-7A)     1467 (POU3F1__RSRFC4)     1492 (HNF-1alpha__POU3F1)     1559 (Chx10__Nkx6-2)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence TAATTA TAATTA
Position frequency matrix
1 2 3 4 5 6
A 0 16 16 0 0 16
C 0 0 0 5 0 0
G 0 0 0 0 0 0
T 16 0 0 11 16 0
T A A T T A
1 2 3 4 5 6
A 0 16 11 0 0 16
C 0 0 0 0 0 0
G 0 0 5 0 0 0
T 16 0 0 16 16 0
T A A T T A

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
ENSMUSG00000061961 Target Mus musculus chr10:129,413,715-129,413,720 + TAATTA – TAATTA
ENSMUSG00000061961_CFAM Orthologue Canis familiaris chr27:3,058,295-3,058,300 – TAATTA + TAATTA
ENSMUSG00000061961_DNOV Orthologue Dasypus novemcinctus scaffold_47683:1,668-1,673 + TAACTA – TAGTTA
ENSMUSG00000061961_DRER Orthologue Danio rerio chr15:35,883,353-35,883,358 – TAATTA + TAATTA
ENSMUSG00000061961_EEUR Orthologue Erinaceus europaeus ENSMUSG00000061961_EEUR:503-508 – TAACTA + TAGTTA
ENSMUSG00000061961_ETEL Orthologue Echinops telfairi scaffold_303156:40,772-40,777 – TAATTA + TAATTA
ENSMUSG00000061961_GGAL Orthologue Gallus gallus chr5:2,414,973-2,414,978 + TAATTA – TAATTA
ENSMUSG00000061961_HSAP Orthologue Homo sapiens chr12:54,150,481-54,150,486 + TAACTA – TAGTTA
ENSMUSG00000061961_LAFR Orthologue Loxodonta africana scaffold_12177:12,965-12,970 + TAATTA – TAATTA
ENSMUSG00000061961_MDOM Orthologue Monodelphis domestica scaffold_33:17,287,712-17,287,717 – TAACTA + TAGTTA
ENSMUSG00000061961_MMUL Orthologue Macaca mulatta SCAFFOLD70084:149,256-149,261 + TAATTA – TAATTA
ENSMUSG00000061961_OCUN Orthologue Oryctolagus cuniculus scaffold_93908:2,224-2,229 + TAATTA – TAATTA
ENSMUSG00000061961_PCAP Orthologue Procavia capensis ENSMUSG00000061961_PCAP:57-62 – TAACTA + TAGTTA
ENSMUSG00000061961_PTRO Orthologue Pan troglodytes chr10:55,236,498-55,236,503 + TAATTA – TAATTA
ENSMUSG00000061961_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000061961_STRI:50-55 – TAATTA + TAATTA
ENSMUSG00000061961_XTRO Orthologue Xenopus tropicalis scaffold_10:4,073,370-4,073,375 + TAATTA – TAATTA

Questions or comments: cisred@bcgsc.ca