FILTERS:
pvalue:0.1
Motif craMmus394644
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 craMmus394644
Discovery p-value 2.79E-03
Motif location chr10: 129,214,141-129,214,152 (+) (12 bp)
Search region location chr10: 129,213,711-129,215,646 (+) (1,936 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 15 species: Mus musculus, Canis familiaris, Dasypus novemcinctus, Echinops telfairi, Fugu rubripes, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Pan troglodytes, Rattus norvegicus, Spermophilus tridecemlineatus, Tupaia belangeri, 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.): Lhx3a(1.80E-04) ,    IPF1(3.50E-04) ,    POU2F1(5.85E-04) ,    STAT1alpha(9.73E-04)
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
55 (Lhx3a__aMEF-2)     74 (IPF1__TEF)     92 (HMG_I__Lhx3a)     151 (IPF1__aMEF-2)     178 (Lhx3a__RSRFC4)     231 (IPF1__IRF-1)     289 (IPF1__Lhx3a)     338 (Chx10__IPF1)     352 (Lhx3a__TEF)     463 (Evi-1__Lhx3a)     636 (IPF1__POU3F2)     709 (IPF1__POU6F1_(c2))     815 (Lhx3a__YY1)     832 (HNF-6__Lhx3a)     845 (IPF1__MEF-2A)     859 (HMG_I__IPF1)     884 (Lhx3a__POU6F1_(c2))     1000 (HNF-1alpha__IPF1)     1022 (FOXP1a__Lhx3a)     1038 (IPF1__RSRFC4)     1118 (HNF-6__IPF1)     1119 (Lhx3a__MEF-2A)     1221 (Evi-1__IPF1)     1241 (IPF1__YY1)     1301 (Lhx3a__Lhx3a)     1323 (IRF-1__Lhx3a)     1400 (HNF-3alpha__IPF1)     1411 (HNF-1alpha__Lhx3a)     1417 (IPF1__Pax-8)     1490 (Lhx3a__POU1F1)     1552 (Chx10__Lhx3a)     1569 (FOXP1a__IPF1)     1574 (IPF1__POU1F1)     1589 (Lhx3a__POU3F2)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence TTnyATTAATwT AsATTAATrnAA
Position frequency matrix
1 2 3 4 5 6 7 8 9 10 11 12
A 3 4 4 2 15 4 0 8 15 0 7 0
C 0 0 0 6 0 0 0 3 0 0 0 0
G 0 0 7 0 0 0 0 0 0 1 0 0
T 12 11 4 7 0 11 15 4 0 14 8 15
T T n y A T T w A T w T
1 2 3 4 5 6 7 8 9 10 11 12
A 15 8 14 0 4 15 11 0 7 4 11 12
C 0 0 1 0 0 0 0 0 0 7 0 0
G 0 0 0 0 3 0 0 0 6 0 0 0
T 0 7 0 15 8 0 4 15 2 4 4 3
A w A T w A A T r n A 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
ENSMUSG00000057403 Target Mus musculus chr10:129,214,141-129,214,152 + TTACATTAATTT – AAATTAATGTAA
ENSMUSG00000057403_CFAM Orthologue Canis familiaris chr27:3,058,469-3,058,480 + TTACAATAATTT – AAATTATTGTAA
ENSMUSG00000057403_DNOV Orthologue Dasypus novemcinctus scaffold_90588:1,600-1,611 – ATGTATTTATAT + ATATAAATACAT
ENSMUSG00000057403_ETEL Orthologue Echinops telfairi scaffold_291129:50,686-50,697 – TTGTATTTATTT + AAATAAATACAA
ENSMUSG00000057403_FRUB Orthologue Fugu rubripes chrUn:265,453,061-265,453,072 + TTACATTTATAT – ATATAAATGTAA
ENSMUSG00000057403_HSAP Orthologue Homo sapiens chr12:53,976,382-53,976,393 + TATTATTCATTT – AAATGAATAATA
ENSMUSG00000057403_LAFR Orthologue Loxodonta africana scaffold_8008:46,282-46,293 + TAGAAATAATAT – ATATTATTTCTA
ENSMUSG00000057403_MDOM Orthologue Monodelphis domestica scaffold_33:18,899,010-18,899,021 – TTGTATTAATAT + ATATTAATACAA
ENSMUSG00000057403_MMUL Orthologue Macaca mulatta SCAFFOLD70084:149,617-149,628 + TTGAAATAAGTT – AACTTATTTCAA
ENSMUSG00000057403_OCUN Orthologue Oryctolagus cuniculus scaffold_93908:2,070-2,081 + TAGCATTAATTT – AAATTAATGCTA
ENSMUSG00000057403_PTRO Orthologue Pan troglodytes chr10:55,236,187-55,236,198 – TTTTATTCATAT + ATATGAATAAAA
ENSMUSG00000057403_RNOR Orthologue Rattus norvegicus chr7:7,052,058-7,052,069 – TTTCATTAATTT + AAATTAATGAAA
ENSMUSG00000057403_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000057403_STRI:157-168 – AAATATTTATTT + AAATAAATATTT
ENSMUSG00000057403_TBEL Orthologue Tupaia belangeri ENSMUSG00000057403_TBEL:63-74 – ATGTAATAATAT + ATATTATTACAT
ENSMUSG00000057403_XTRO Orthologue Xenopus tropicalis scaffold_10:4,549,099-4,549,110 + TTTCATTCATAT – ATATGAATGAAA

Questions or comments: cisred@bcgsc.ca