FILTERS:
pvalue:0.1
Motif craMmus345655
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 craMmus345655
Discovery p-value 2.79E-03
Motif location chr18: 37,864,464-37,864,473 (+) (10 bp)
Search region location chr18: 37,864,166-37,865,865 (+) (1,700 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 14 species: Mus musculus, Dasypus novemcinctus, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Macaca mulatta, Oryctolagus cuniculus, Pan troglodytes, Rattus norvegicus, Sorex araneus, 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 6 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (6 annot.): HNF-3alpha(9.89E-05) ,    HNF-3(4.50E-04) ,    TEF(4.52E-04) ,    POU1F1(5.16E-04) ,    HNF-3(5.61E-04) ...
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence wwrAATAAAC GTTTATTyss
Position frequency matrix
1 2 3 4 5 6 7 8 9 10
A 8 6 9 14 14 0 14 14 14 4
C 0 0 0 0 0 2 0 0 0 8
G 0 0 5 0 0 0 0 0 0 2
T 6 8 0 0 0 12 0 0 0 0
w w n A A T A A A m
1 2 3 4 5 6 7 8 9 10
A 0 0 0 0 12 0 0 0 8 6
C 2 0 0 0 0 0 0 5 0 0
G 8 0 0 0 2 0 0 0 0 0
T 4 14 14 14 0 14 14 9 6 8
k T T T A T T n w w

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
ENSMUSG00000048347 Target Mus musculus chr18:37,864,464-37,864,473 + TTGAATAAAC – GTTTATTCAA
ENSMUSG00000048347_DNOV Orthologue Dasypus novemcinctus scaffold_35329:4,826-4,835 + TTGAATAAAG – CTTTATTCAA
ENSMUSG00000048347_FRUB Orthologue Fugu rubripes chrUn:6,136,932-6,136,941 – ATAAATAAAA + TTTTATTTAT
ENSMUSG00000048347_GGAL Orthologue Gallus gallus chrUn:36,704,980-36,704,989 – AAAAATAAAA + TTTTATTTTT
ENSMUSG00000048347_HSAP Orthologue Homo sapiens chr5:140,550,334-140,550,343 + ATAAATAAAC – GTTTATTTAT
ENSMUSG00000048347_LAFR Orthologue Loxodonta africana scaffold_83811:6,163-6,172 + AAAAATAAAC – GTTTATTTTT
ENSMUSG00000048347_MMUL Orthologue Macaca mulatta SCAFFOLD30831:31,166-31,175 – TAAAATAAAC + GTTTATTTTA
ENSMUSG00000048347_OCUN Orthologue Oryctolagus cuniculus scaffold_198387:93,655-93,664 – TTGAATAAAA + TTTTATTCAA
ENSMUSG00000048347_PTRO Orthologue Pan troglodytes chr4:147,180,097-147,180,106 – ATAAATAAAC + GTTTATTTAT
ENSMUSG00000048347_RNOR Orthologue Rattus norvegicus chr18:30,326,526-30,326,535 + TTGAATAAAC – GTTTATTCAA
ENSMUSG00000048347_SARA Orthologue Sorex araneus ENSMUSG00000048347_SARA:372-381 + AAAAACAAAC – GTTTGTTTTT
ENSMUSG00000048347_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000048347_STRI:533-542 + ATGAATAAAC – GTTTATTCAT
ENSMUSG00000048347_TBEL Orthologue Tupaia belangeri ENSMUSG00000048347_TBEL:130-139 + AAAAACAAAA – TTTTGTTTTT
ENSMUSG00000048347_XTRO Orthologue Xenopus tropicalis scaffold_15:3,901,308-3,901,317 + TAAAATAAAG – CTTTATTTTA

Questions or comments: cisred@bcgsc.ca