FILTERS:
pvalue:0.1
Motif craMmus291683
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 craMmus291683
Discovery p-value 2.79E-03
Motif location chr7: 82,205,932-82,205,941 (-) (10 bp)
Search region location chr7: 82,204,740-82,206,517 (-) (1,778 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 16 species: Mus musculus, Bos taurus, Canis familiaris, Dasypus novemcinctus, Danio rerio, Echinops telfairi, Fugu rubripes, Homo sapiens, Loxodonta africana, Macaca mulatta, Oryctolagus cuniculus, Pan troglodytes, Rattus norvegicus, Sorex araneus, 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 14 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (8 annot.): Nkx2-2(1.08E-04) ,    Nkx3-1(1.43E-04) ,    HOXA5(2.41E-04) ,    S8(2.63E-04) ,    E4BP4(3.15E-04) ...
ORegAnno: (6 annot.): FoxA1(2.03E-04) ,    FoxA1(3.76E-04) ,    FoxA1(3.76E-04) ,    FoxA1(4.74E-04) ,    FoxA1(4.74E-04) ...
Modules
(Co-occurring motif patterns)		 Annotation-based:
211 (E4BP4__aMEF-2)     217 (Nkx3-1__aMEF-2)     261 (Chx10__E4BP4)     265 (Chx10__MEF-2A)     281 (Nkx3-1__S8)     435 (HOXA5__MEF-2A)     498 (Chx10__HOXA5)     516 (E4BP4__IRF-1)     536 (Chx10__HNF-1alpha)     543 (E4BP4__HNF-1alpha)     578 (E4BP4__Nkx6-2)     603 (Nkx2-2__aMEF-2)     691 (HOXA5__Nkx3-1)     707 (Chx10__S8)     732 (Nkx3-1__Nkx3-1)     875 (HOXA5__Nkx6-2)     905 (IRF-1__Nkx3-1)     940 (HNF-1alpha__Nkx3-1)     1010 (Chx10__Nkx3-1)     1013 (Nkx6-2__S8)     1037 (E4BP4__Nkx3-1)     1062 (HNF-1alpha__HOXA5)     1147 (HNF-1alpha__S8)     1152 (E4BP4__MEF-2A)     1161 (Chx10__Nkx2-2)     1207 (Chx10__IRF-1)     1287 (Nkx3-1__Nkx6-2)     1337 (IRF-1__S8)     1356 (HOXA5__IRF-1)     1394 (Chx10__Chx10)     1450 (S8__aMEF-2)     1464 (HOXA5__aMEF-2)     1469 (MEF-2A__Nkx3-1)     1471 (Chx10__aMEF-2)     1559 (Chx10__Nkx6-2)     1601 (MEF-2A__S8)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence AAsTATkTAT ATAmATAwTT
Position frequency matrix
1 2 3 4 5 6 7 8 9 10
A 13 14 6 0 16 0 0 2 14 0
C 0 2 0 0 0 4 0 0 0 0
G 0 0 0 0 0 1 8 0 0 0
T 3 0 10 16 0 11 8 14 2 16
A A n T A T k T A T
1 2 3 4 5 6 7 8 9 10
A 16 2 14 8 11 0 16 10 0 3
C 0 0 0 8 1 0 0 0 0 0
G 0 0 0 0 4 0 0 0 2 0
T 0 14 2 0 0 16 0 6 14 13
A T A m A T A n T T

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
ENSMUSG00000057540 Target Mus musculus chr7:82,205,932-82,205,941 + AATTACTTAT – ATAAGTAATT
ENSMUSG00000057540_BTAU Orthologue Bos taurus chr1:22,331,395-22,331,404 + AAATATGTAT – ATACATATTT
ENSMUSG00000057540_CFAM Orthologue Canis familiaris chr14:5,335,020-5,335,029 + AAATATGTAT – ATACATATTT
ENSMUSG00000057540_DNOV Orthologue Dasypus novemcinctus scaffold_39105:3,858-3,867 + AATTACTTAT – ATAAGTAATT
ENSMUSG00000057540_DRER Orthologue Danio rerio chr15:36,047,902-36,047,911 + TAATATGTAT – ATACATATTA
ENSMUSG00000057540_ETEL Orthologue Echinops telfairi scaffold_267478:3,574-3,583 – AATTATTTAT + ATAAATAATT
ENSMUSG00000057540_FRUB Orthologue Fugu rubripes chrUn:198,145,018-198,145,027 + TCTTACGTAT – ATACGTAAGA
ENSMUSG00000057540_HSAP Orthologue Homo sapiens chr1:244,837,754-244,837,763 – AATTATTTAT + ATAAATAATT
ENSMUSG00000057540_LAFR Orthologue Loxodonta africana scaffold_13355:22,037-22,046 + AATTATGTAT – ATACATAATT
ENSMUSG00000057540_MMUL Orthologue Macaca mulatta SCAFFOLD478:4,384-4,393 + AATTAGTTAT – ATAACTAATT
ENSMUSG00000057540_OCUN Orthologue Oryctolagus cuniculus scaffold_177791:107,406-107,415 – AATTACTAAT + ATTAGTAATT
ENSMUSG00000057540_PTRO Orthologue Pan troglodytes chr1:228,895,786-228,895,795 + AATTATTATT – AATAATAATT
ENSMUSG00000057540_RNOR Orthologue Rattus norvegicus chr1:142,617,010-142,617,019 – AAATATTTAT + ATAAATATTT
ENSMUSG00000057540_SARA Orthologue Sorex araneus ENSMUSG00000057540_SARA:49-58 + AAATATGTTT – AAACATATTT
ENSMUSG00000057540_TNIG Orthologue Tetraodon nigroviridis Un_random:124,234,036-124,234,045 – AAATATGTAT + ATACATATTT
ENSMUSG00000057540_XTRO Orthologue Xenopus tropicalis scaffold_7:3,160,191-3,160,200 + TCTTATGTAT – ATACATAAGA

Questions or comments: cisred@bcgsc.ca