FILTERS:
pvalue:0.1
Motif craMmus207776
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 craMmus207776
Discovery p-value 7.38E-02
Motif location chr6: 28,330,107-28,330,116 (-) (10 bp)
Search region location chr6: 28,329,922-28,333,017 (-) (3,096 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 14 species: Mus musculus, Canis familiaris, Cavia porcellus, Gallus gallus, Homo sapiens, Loxodonta africana, Macaca mulatta, Oryctolagus cuniculus, Procavia capensis, Pan troglodytes, Rattus norvegicus, Sus scrofa, Spermophilus tridecemlineatus, Tupaia belangeri
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 3 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (3 annot.): Brachyury(2.89E-04) ,    AP-4(3.95E-04) ,    E12(9.20E-04)
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 No annotation-based modules contain this motif.
No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence GCTGCAGCnG CnGCTGCAGC
Position frequency matrix
1 2 3 4 5 6 7 8 9 10
A 1 0 1 0 0 14 0 0 4 2
C 1 13 0 0 14 0 0 13 4 1
G 12 0 0 14 0 0 14 1 0 11
T 0 1 13 0 0 0 0 0 6 0
G C T G C A G C n G
1 2 3 4 5 6 7 8 9 10
A 0 6 0 0 0 0 0 13 1 0
C 11 0 1 14 0 0 14 0 0 12
G 1 4 13 0 0 14 0 0 13 1
T 2 4 0 0 14 0 0 1 0 1
C n G C T G C A G C

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
ENSMUSG00000039841 Target Mus musculus chr6:28,330,107-28,330,116 + GCTGCAGCAA – TTGCTGCAGC
ENSMUSG00000039841_CFAM Orthologue Canis familiaris chr14:11,722,025-11,722,034 + ACTGCAGCTG – CAGCTGCAGT
ENSMUSG00000039841_CPOR Orthologue Cavia porcellus ENSMUSG00000039841_CPOR:81-90 + GCAGCAGCTG – CAGCTGCTGC
ENSMUSG00000039841_GGAL Orthologue Gallus gallus chr1:17,720,001-17,720,010 + GTTGCAGCTG – CAGCTGCAAC
ENSMUSG00000039841_HSAP Orthologue Homo sapiens chr7:126,771,014-126,771,023 + GCTGCAGCCG – CGGCTGCAGC
ENSMUSG00000039841_LAFR Orthologue Loxodonta africana scaffold_63584:8,094-8,103 + GCTGCAGCTC – GAGCTGCAGC
ENSMUSG00000039841_MMUL Orthologue Macaca mulatta SCAFFOLD265:23,909-23,918 + GCTGCAGCCG – CGGCTGCAGC
ENSMUSG00000039841_OCUN Orthologue Oryctolagus cuniculus scaffold_151765:9,150-9,159 – GCTGCAGCTG + CAGCTGCAGC
ENSMUSG00000039841_PCAP Orthologue Procavia capensis ENSMUSG00000039841_PCAP:348-357 – GCTGCAGCAA + TTGCTGCAGC
ENSMUSG00000039841_PTRO Orthologue Pan troglodytes chr6:129,184,216-129,184,225 + GCTGCAGCCG – CGGCTGCAGC
ENSMUSG00000039841_RNOR Orthologue Rattus norvegicus chr4:55,517,168-55,517,177 – GCTGCAGCTG + CAGCTGCAGC
ENSMUSG00000039841_SSCR Orthologue Sus scrofa ENSMUSG00000039841_SSCR:503-512 – GCTGCAGCCG + CGGCTGCAGC
ENSMUSG00000039841_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000039841_STRI:18-27 – CCTGCAGCAG + CTGCTGCAGG
ENSMUSG00000039841_TBEL Orthologue Tupaia belangeri ENSMUSG00000039841_TBEL:317-326 – GCTGCAGGAG + CTCCTGCAGC

Questions or comments: cisred@bcgsc.ca