FILTERS:
pvalue:0.1
Motif craMmus296363
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 craMmus296363
Discovery p-value 2.79E-03
Motif location chr7: 104,480,853-104,480,862 (-) (10 bp)
Search region location chr7: 104,480,550-104,482,249 (-) (1,700 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 16 species: Mus musculus, Bos taurus, Cavia porcellus, Dasypus novemcinctus, Danio rerio, Echinops telfairi, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Pan troglodytes, Rattus norvegicus, Sus scrofa, Spermophilus tridecemlineatus, Tetraodon nigroviridis
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 7 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (6 annot.): HNF-1alpha(1.03E-04) ,    RSRFC4(5.40E-04) ,    RSRFC4(5.92E-04) ,    HNF-3alpha(8.46E-04) ,    HNF-3(8.62E-04) ...
ORegAnno: (1 annot.): FoxA1(6.44E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence TAAATAsATA TATwTATTTA
Position frequency matrix
1 2 3 4 5 6 7 8 9 10
A 0 11 15 15 2 16 8 13 0 13
C 0 0 0 0 3 0 0 0 0 0
G 0 0 1 1 0 0 0 0 3 0
T 16 5 0 0 11 0 8 3 13 3
T A A A T A w A T A
1 2 3 4 5 6 7 8 9 10
A 3 13 3 8 0 11 0 0 5 16
C 0 3 0 0 0 0 1 1 0 0
G 0 0 0 0 0 3 0 0 0 0
T 13 0 13 8 16 2 15 15 11 0
T A T w T A T T T 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
ENSMUSG00000060105 Target Mus musculus chr7:104,480,853-104,480,862 + TTAATAAATA – TATTTATTAA
ENSMUSG00000060105_BTAU Orthologue Bos taurus chr21:39,469,274-39,469,283 + TAAATATAGT – ACTATATTTA
ENSMUSG00000060105_CPOR Orthologue Cavia porcellus ENSMUSG00000060105_CPOR:120-129 – TTAAAATAGA + TCTATTTTAA
ENSMUSG00000060105_DNOV Orthologue Dasypus novemcinctus scaffold_42612:4,055-4,064 + TTAGTAAAGA – TCTTTACTAA
ENSMUSG00000060105_DRER Orthologue Danio rerio chr15:35,996,951-35,996,960 + TAAACAAATA – TATTTGTTTA
ENSMUSG00000060105_ETEL Orthologue Echinops telfairi scaffold_320604:102,782-102,791 + TAAATAATTT – AAATTATTTA
ENSMUSG00000060105_HSAP Orthologue Homo sapiens chr11:5,712,760-5,712,769 – TAAACATATA + TATATGTTTA
ENSMUSG00000060105_LAFR Orthologue Loxodonta africana scaffold_140:172,208-172,217 – TAGATAAATA + TATTTATCTA
ENSMUSG00000060105_MDOM Orthologue Monodelphis domestica scaffold_33:19,317,134-19,317,143 + TTAATATATT – AATATATTAA
ENSMUSG00000060105_MMUL Orthologue Macaca mulatta SCAFFOLD76760:11,850-11,859 – TAAACATATA + TATATGTTTA
ENSMUSG00000060105_OCUN Orthologue Oryctolagus cuniculus scaffold_111774:3,683-3,692 + TAAATAAATA – TATTTATTTA
ENSMUSG00000060105_PTRO Orthologue Pan troglodytes chr9:5,847,858-5,847,867 + TAAATAAATA – TATTTATTTA
ENSMUSG00000060105_RNOR Orthologue Rattus norvegicus chr1:162,382,562-162,382,571 – TAAATATATA + TATATATTTA
ENSMUSG00000060105_SSCR Orthologue Sus scrofa ENSMUSG00000060105_SSCR:68-77 – TAAAAATATA + TATATTTTTA
ENSMUSG00000060105_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000060105_STRI:33-42 + TTAATAATTA – TAATTATTAA
ENSMUSG00000060105_TNIG Orthologue Tetraodon nigroviridis Un_random:115,318,034-115,318,043 – TAAATATTTA + TAAATATTTA

Questions or comments: cisred@bcgsc.ca