FILTERS:
pvalue:0.1
Motif craMmus336922
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 craMmus336922
Discovery p-value 2.79E-03
Motif location chr2: 87,867,917-87,867,928 (+) (12 bp)
Search region location chr2: 87,866,875-87,868,639 (+) (1,765 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 17 species: Mus musculus, Canis familiaris, Cavia porcellus, Dasypus novemcinctus, Danio rerio, Erinaceus europaeus, Echinops telfairi, Fugu rubripes, Homo sapiens, Loxodonta africana, Monodelphis domestica, Oryctolagus cuniculus, Otolemur garnettii, Procavia capensis, Pan troglodytes, Rattus norvegicus, Tetraodon nigroviridis
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: (5 annot.): POU1F1(1.44E-05) ,    POU3F2(8.57E-05) ,    HOXA5(1.69E-04) ,    POU1F1(5.16E-04) ,    YY1(7.03E-04)
ORegAnno: (1 annot.): FoxA1(9.28E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
26 (HOXA5__Sox5)     39 (Cdx-2__HOXA5)     53 (POU1F1__aMEF-2)     59 (POU1F1__POU1F1)     160 (POU1F1__POU3F2)     161 (Brachyury__HOXA5)     177 (Brachyury__POU3F2)     226 (POU3F2__S8)     233 (AIRE__POU1F1)     252 (POU3F2__POU3F2)     282 (FOXP1a__POU3F2)     339 (HOXA5__S8)     340 (Cdx-2__POU3F2)     343 (POU1F1__S8)     361 (HOXA5__POU3F2)     399 (POU3F2__aMEF-2)     465 (HOXA5__RSRFC4)     472 (Brachyury__POU1F1)     477 (HOXA5__POU1F1)     492 (Evi-1__POU3F2)     498 (Chx10__HOXA5)     514 (AIRE__HOXA5)     611 (Chx10__POU1F1)     636 (IPF1__POU3F2)     786 (POU3F2__Sox5)     904 (HOXA5__IPF1)     944 (POU3F2__RSRFC4)     1025 (HOXA5__Lhx3a)     1044 (Cdx-2__POU1F1)     1062 (HNF-1alpha__HOXA5)     1075 (FOXO4__POU3F2)     1135 (HOXA5__TEF)     1167 (POU3F2__TEF)     1185 (AIRE__POU3F2)     1196 (POU1F1__TEF)     1243 (POU1F1__Sox5)     1333 (Evi-1__POU1F1)     1340 (FOXP1a__POU1F1)     1363 (POU1F1__RSRFC4)     1412 (FOXP1a__HOXA5)     1439 (Evi-1__HOXA5)     1442 (Chx10__POU3F2)     1464 (HOXA5__aMEF-2)     1476 (HNF-1alpha__POU3F2)     1490 (Lhx3a__POU1F1)     1574 (IPF1__POU1F1)     1589 (Lhx3a__POU3F2)     1600 (HNF-1alpha__POU1F1)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence ATwAwTGwATTT AAATsCAsTsAT
Position frequency matrix
1 2 3 4 5 6 7 8 9 10 11 12
A 13 0 9 17 6 0 0 7 9 3 4 5
C 0 0 0 0 0 0 0 0 4 0 0 0
G 0 0 1 0 0 0 13 0 2 0 0 0
T 4 17 7 0 11 17 4 10 2 14 13 12
A T w A n T G w m T T T
1 2 3 4 5 6 7 8 9 10 11 12
A 12 13 14 2 10 4 17 11 0 7 17 4
C 0 0 0 2 0 13 0 0 0 1 0 0
G 0 0 0 4 0 0 0 0 0 0 0 0
T 5 4 3 9 7 0 0 6 17 9 0 13
A A A k w C A n T w 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
ENSMUSG00000045150 Target Mus musculus chr2:87,867,917-87,867,928 + ATTAATGAATAT – ATATTCATTAAT
ENSMUSG00000045150_CFAM Orthologue Canis familiaris chr18:43,169,775-43,169,786 + ATTATTGACTTT – AAAGTCAATAAT
ENSMUSG00000045150_CPOR Orthologue Cavia porcellus ENSMUSG00000045150_CPOR:176-187 + ATAAATGTCATA – TATGACATTTAT
ENSMUSG00000045150_DNOV Orthologue Dasypus novemcinctus scaffold_22184:11,264-11,275 – ATTAATTTATTT + AAATAAATTAAT
ENSMUSG00000045150_DRER Orthologue Danio rerio chr10:33,722,033-33,722,044 – ATAAATGAATTT + AAATTCATTTAT
ENSMUSG00000045150_EEUR Orthologue Erinaceus europaeus ENSMUSG00000045150_EEUR:397-408 + ATGATTGTCATA – TATGACAATCAT
ENSMUSG00000045150_ETEL Orthologue Echinops telfairi scaffold_272748:12,016-12,027 – ATTAATGTATTT + AAATACATTAAT
ENSMUSG00000045150_FRUB Orthologue Fugu rubripes chrUn:265,456,372-265,456,383 + TTAAATGTGTAT – ATACACATTTAA
ENSMUSG00000045150_HSAP Orthologue Homo sapiens chr11:55,343,466-55,343,477 + ATAATTGTATTT – AAATACAATTAT
ENSMUSG00000045150_LAFR Orthologue Loxodonta africana scaffold_8:263,005-263,016 – ATAATTTATTTT + AAAATAAATTAT
ENSMUSG00000045150_MDOM Orthologue Monodelphis domestica scaffold_33:17,123,261-17,123,272 – TTAATTGAATAT + ATATTCAATTAA
ENSMUSG00000045150_OCUN Orthologue Oryctolagus cuniculus scaffold_212637:2,380-2,391 + ATTATTGAATTA – TAATTCAATAAT
ENSMUSG00000045150_OGAR Orthologue Otolemur garnettii ENSMUSG00000045150_OGAR:29-40 + TTTATTTTCTTT – AAAGAAAATAAA
ENSMUSG00000045150_PCAP Orthologue Procavia capensis ENSMUSG00000045150_PCAP:171-182 + ATAATTTAGATA – TATCTAAATTAT
ENSMUSG00000045150_PTRO Orthologue Pan troglodytes chr9:56,243,825-56,243,836 + ATAATTGTATTT – AAATACAATTAT
ENSMUSG00000045150_RNOR Orthologue Rattus norvegicus chr3:71,662,297-71,662,308 – ATTATTGTATAA + TTATACAATAAT
ENSMUSG00000045150_TNIG Orthologue Tetraodon nigroviridis chr2:14,427,899-14,427,910 + TTAATTGTTTTT – AAAAACAATTAA

Questions or comments: cisred@bcgsc.ca