FILTERS:
pvalue:0.1
Motif craMmus62287
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 craMmus62287
Discovery p-value 2.79E-03
Motif location chr10: 129,250,267-129,250,274 (-) (8 bp)
Search region location chr10: 129,249,283-129,250,982 (-) (1,700 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 14 species: Mus musculus, Canis familiaris, Dasypus novemcinctus, Danio rerio, Echinops telfairi, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Pan troglodytes, Tetraodon nigroviridis, Xenopus tropicalis
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 4 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (4 annot.): FOXJ2(3.49E-05) ,    Cdx-2(2.79E-04) ,    FOXD3(3.07E-04) ,    CUTL1(3.56E-04)
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
12 (Evi-1__FOXJ2)     14 (AIRE__FOXJ2)     18 (FOXD3__aMEF-2)     25 (FOXJ2__Lhx3a)     31 (CUTL1__POU6F1_(c2))     44 (CUTL1__Evi-1)     51 (Cdx-2__FOXP1a)     91 (Cdx-2__RSRFC4)     98 (Cdx-2__IRF-1)     124 (Cdx-2__Evi-1)     138 (FOXJ2__RSRFC4)     166 (FOXD3__Nkx6-2)     203 (CUTL1__Nkx3-1)     206 (AFP1__FOXD3)     245 (FOXJ2__FOXP1a)     254 (Cdx-2__Chx10)     271 (CUTL1__RSRFC4)     292 (Cdx-2__aMEF-2)     298 (FOXJ2__TEF)     314 (AFP1__FOXJ2)     319 (FOXD3__IRF-1)     320 (CUTL1__TEF)     329 (CUTL1__Chx10)     340 (Cdx-2__POU3F2)     376 (Evi-1__FOXD3)     384 (Chx10__FOXJ2)     391 (CUTL1__POU3F2)     393 (CUTL1__POU2F1)     452 (FOXJ2__Nkx3-1)     566 (FOXJ2__Nkx6-2)     621 (Cdx-2__TEF)     642 (Cdx-2__Nkx3-1)     657 (FOXD3__POU1F1)     658 (CUTL1__Lhx3a)     727 (FOXD3__TEF)     733 (CUTL1__OCA-B)     787 (CUTL1__aMEF-2)     816 (CUTL1__IRF-1)     874 (FOXJ2__IRF-1)     880 (CUTL1__POU1F1)     881 (AFP1__CUTL1)     916 (Cdx-2__POU2F1)     922 (FOXJ2__POU2F1)     1007 (FOXD3__POU3F2)     1016 (FOXJ2__POU6F1_(c2))     1018 (FOXD3__POU6F1_(c2))     1034 (FOXD3__POU2F1)     1036 (AIRE__Cdx-2)     1044 (Cdx-2__POU1F1)     1077 (Cdx-2__OCA-B)     1080 (AIRE__CUTL1)     1110 (FOXJ2__POU1F1)     1151 (FOXJ2__MEF-2A)     1219 (FOXD3__Nkx3-1)     1231 (Cdx-2__MEF-2A)     1233 (FOXJ2__POU3F2)     1255 (Cdx-2__Nkx6-2)     1293 (FOXD3__RSRFC4)     1300 (CUTL1__LEF-1)     1358 (CUTL1__Nkx6-2)     1376 (CUTL1__FOXP1a)     1378 (FOXD3__MEF-2A)     1387 (FOXD3__FOXP1a)     1407 (CUTL1__MEF-2A)     1409 (Cdx-2__Lhx3a)     1410 (Cdx-2__POU6F1_(c2))     1433 (FOXJ2__OCA-B)     1547 (AFP1__Cdx-2)     1564 (FOXJ2__aMEF-2)     1592 (Chx10__FOXD3)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence ATATrTAT ATAyATAT
Position frequency matrix
1 2 3 4 5 6 7 8
A 12 0 14 0 5 0 14 0
C 2 0 0 2 0 0 0 0
G 0 0 0 0 6 0 0 0
T 0 14 0 12 3 14 0 14
A T A T r T A T
1 2 3 4 5 6 7 8
A 14 0 14 3 12 0 14 0
C 0 0 0 6 0 0 0 0
G 0 0 0 0 2 0 0 2
T 0 14 0 5 0 14 0 12
A T A y 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
ENSMUSG00000071065 Target Mus musculus chr10:129,250,267-129,250,274 + ATATTTAT – ATAAATAT
ENSMUSG00000071065_CFAM Orthologue Canis familiaris chr27:3,057,989-3,057,996 + ATATATAT – ATATATAT
ENSMUSG00000071065_DNOV Orthologue Dasypus novemcinctus scaffold_30084:2,023-2,030 – ATATATAT + ATATATAT
ENSMUSG00000071065_DRER Orthologue Danio rerio chr15:36,003,634-36,003,641 + ATATATAT – ATATATAT
ENSMUSG00000071065_ETEL Orthologue Echinops telfairi scaffold_303156:40,207-40,214 + ATATGTAT – ATACATAT
ENSMUSG00000071065_GGAL Orthologue Gallus gallus chr5:2,413,794-2,413,801 – ATACGTAT + ATACGTAT
ENSMUSG00000071065_HSAP Orthologue Homo sapiens chr12:53,962,476-53,962,483 + ATATGTAT – ATACATAT
ENSMUSG00000071065_LAFR Orthologue Loxodonta africana scaffold_8008:45,198-45,205 – ATATTTAT + ATAAATAT
ENSMUSG00000071065_MDOM Orthologue Monodelphis domestica scaffold_33:17,004,209-17,004,216 – CTATGTAT + ATACATAG
ENSMUSG00000071065_MMUL Orthologue Macaca mulatta SCAFFOLD70084:150,683-150,690 – ATATGTAT + ATACATAT
ENSMUSG00000071065_OCUN Orthologue Oryctolagus cuniculus scaffold_93908:1,260-1,267 – CTATGTAT + ATACATAG
ENSMUSG00000071065_PTRO Orthologue Pan troglodytes chr10:55,236,774-55,236,781 – ATATATAT + ATATATAT
ENSMUSG00000071065_TNIG Orthologue Tetraodon nigroviridis Un_random:115,317,991-115,317,998 + ATACATAT – ATATGTAT
ENSMUSG00000071065_XTRO Orthologue Xenopus tropicalis scaffold_10:4,401,597-4,401,604 + ATATTTAT – ATAAATAT

Questions or comments: cisred@bcgsc.ca