FILTERS:
pvalue:0.1
Motif craMmus59678
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 craMmus59678
Discovery p-value 2.79E-03
Motif location chr19: 12,792,612-12,792,621 (-) (10 bp)
Search region location chr19: 12,792,203-12,793,994 (-) (1,792 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 14 species: Mus musculus, Canis familiaris, Dasypus novemcinctus, Echinops telfairi, Fugu rubripes, Homo sapiens, Loxodonta africana, Monodelphis domestica, Oryctolagus cuniculus, Pan troglodytes, Rattus norvegicus, Spermophilus tridecemlineatus, 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 9 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (8 annot.): HOXA5(1.72E-04) ,    POU2F1(3.49E-04) ,    IPF1(5.26E-04) ,    RSRFC4(8.10E-04) ,    HNF-1alpha(8.30E-04) ...
ORegAnno: (1 annot.): FoxA1(9.65E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence TsmAsTGTsT AwACAwTkwA
Position frequency matrix
1 2 3 4 5 6 7 8 9 10
A 3 5 6 14 9 0 0 3 8 4
C 0 0 8 0 0 0 0 0 0 0
G 0 0 0 0 0 0 14 0 0 2
T 11 9 0 0 5 14 0 11 6 8
T n m A n T G T w w
1 2 3 4 5 6 7 8 9 10
A 8 6 11 0 14 5 0 0 9 11
C 2 0 0 14 0 0 0 0 0 0
G 0 0 0 0 0 0 0 8 0 0
T 4 8 3 0 0 9 14 6 5 3
w w A C A n T k n 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
ENSMUSG00000061637 Target Mus musculus chr19:12,792,612-12,792,621 + TTAATTGTTT – AAACAATTAA
ENSMUSG00000061637_CFAM Orthologue Canis familiaris chr18:41,020,237-41,020,246 – TTCAATGTAA + TTACATTGAA
ENSMUSG00000061637_DNOV Orthologue Dasypus novemcinctus scaffold_170430:764-773 – TAAATTGTAA + TTACAATTTA
ENSMUSG00000061637_ETEL Orthologue Echinops telfairi scaffold_232072:3,432-3,441 – TACAATGAAG + CTTCATTGTA
ENSMUSG00000061637_FRUB Orthologue Fugu rubripes chrUn:265,468,864-265,468,873 – TTCAATGATT + AATCATTGAA
ENSMUSG00000061637_HSAP Orthologue Homo sapiens chr11:57,885,100-57,885,109 + TACATTGATT – AATCAATGTA
ENSMUSG00000061637_LAFR Orthologue Loxodonta africana scaffold_26148:24,866-24,875 – ATCATTGTAT + ATACAATGAT
ENSMUSG00000061637_MDOM Orthologue Monodelphis domestica scaffold_33:22,363,586-22,363,595 + TACAATGTAT – ATACATTGTA
ENSMUSG00000061637_OCUN Orthologue Oryctolagus cuniculus scaffold_141326:6,324-6,333 – TAAATTGTAT + ATACAATTTA
ENSMUSG00000061637_PTRO Orthologue Pan troglodytes 9_random:27,934,696-27,934,705 + ATCAATGTAG – CTACATTGAT
ENSMUSG00000061637_RNOR Orthologue Rattus norvegicus chr1:216,494,648-216,494,657 – TTAAATGTTT + AAACATTTAA
ENSMUSG00000061637_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000061637_STRI:342-351 – TTCAATGTAA + TTACATTGAA
ENSMUSG00000061637_TNIG Orthologue Tetraodon nigroviridis chr2:14,428,415-14,428,424 – TTAAATGTTA + TAACATTTAA
ENSMUSG00000061637_XTRO Orthologue Xenopus tropicalis scaffold_94:2,136,997-2,137,006 + ATAAATGTTT – AAACATTTAT

Questions or comments: cisred@bcgsc.ca