FILTERS:
pvalue:0.1
Motif craMmus334061
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 craMmus334061
Discovery p-value 2.79E-03
Motif location chr2: 87,261,527-87,261,532 (+) (6 bp)
Search region location chr2: 87,260,197-87,261,965 (+) (1,769 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 19 species: Mus musculus, Bos taurus, Canis familiaris, Danio rerio, Erinaceus europaeus, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Myotis lucifugus, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, Procavia capensis, Rattus norvegicus, Tupaia belangeri, 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.): aMEF-2(1.65E-04) ,    HNF-3(3.55E-04) ,    RSRFC4(3.65E-04) ,    Evi-1(4.59E-04) ,    RSRFC4(4.71E-04) ...
ORegAnno: (1 annot.): FoxA1(5.39E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
3 (IRF-1__aMEF-2)     11 (Nkx2-5__RSRFC4)     22 (Brachyury__aMEF-2)     46 (HNF-3__POU6F1_(c2))     53 (POU1F1__aMEF-2)     61 (Nkx2-5__aMEF-2)     185 (HNF-1alpha__HNF-3)     219 (HNF-1alpha__RSRFC4)     250 (POU6F1_(c2)__RSRFC4)     270 (Evi-1__HNF-3)     284 (Brachyury__HNF-3)     317 (POU6F1_(c2)__aMEF-2)     350 (AIRE__HNF-3)     369 (RSRFC4__Sox9)     399 (POU3F2__aMEF-2)     446 (Evi-1__RSRFC4)     465 (HOXA5__RSRFC4)     723 (HNF-3__Sox9)     767 (HNF-1alpha__aMEF-2)     797 (Sox9__aMEF-2)     850 (FOXP3__aMEF-2)     858 (HNF-3__POU3F2)     869 (Evi-1__aMEF-2)     934 (RSRFC4__aMEF-2)     944 (POU3F2__RSRFC4)     987 (Brachyury__RSRFC4)     1003 (HNF-3__POU1F1)     1060 (HNF-3__IRF-1)     1238 (HNF-3__HOXA5)     1329 (FOXP3__RSRFC4)     1363 (POU1F1__RSRFC4)     1428 (HNF-3__aMEF-2)     1429 (Chx10__RSRFC4)     1446 (IRF-1__RSRFC4)     1464 (HOXA5__aMEF-2)     1471 (Chx10__aMEF-2)     1503 (Chx10__HNF-3)     1504 (aMEF-2__aMEF-2)     1523 (AIRE__aMEF-2)     1529 (AIRE__RSRFC4)     1587 (FOXP3__HNF-3)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence AATTAT ATAATT
Position frequency matrix
1 2 3 4 5 6
A 19 19 6 0 19 0
C 0 0 0 0 0 0
G 0 0 0 0 0 0
T 0 0 13 19 0 19
A A T T A T
1 2 3 4 5 6
A 19 0 19 13 0 0
C 0 0 0 0 0 0
G 0 0 0 0 0 0
T 0 19 0 6 19 19
A T A A 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
ENSMUSG00000043274 Target Mus musculus chr2:87,261,527-87,261,532 + AAATAT – ATATTT
ENSMUSG00000043274_BTAU Orthologue Bos taurus chr2:606,332-606,337 – AATTAT + ATAATT
ENSMUSG00000043274_CFAM Orthologue Canis familiaris chr18:42,956,736-42,956,741 – AATTAT + ATAATT
ENSMUSG00000043274_DRER Orthologue Danio rerio chr10:33,701,172-33,701,177 – AATTAT + ATAATT
ENSMUSG00000043274_EEUR Orthologue Erinaceus europaeus ENSMUSG00000043274_EEUR:157-162 – AAATAT + ATATTT
ENSMUSG00000043274_FRUB Orthologue Fugu rubripes chrUn:304,389,835-304,389,840 + AATTAT – ATAATT
ENSMUSG00000043274_GGAL Orthologue Gallus gallus chr5:57,961-57,966 – AATTAT + ATAATT
ENSMUSG00000043274_HSAP Orthologue Homo sapiens chr11:55,493,931-55,493,936 + AATTAT – ATAATT
ENSMUSG00000043274_LAFR Orthologue Loxodonta africana scaffold_28824:1,138-1,143 + AAATAT – ATATTT
ENSMUSG00000043274_MDOM Orthologue Monodelphis domestica scaffold_33:17,444,869-17,444,874 + AATTAT – ATAATT
ENSMUSG00000043274_MLUC Orthologue Myotis lucifugus ENSMUSG00000043274_MLUC:195-200 – AAATAT + ATATTT
ENSMUSG00000043274_MMUL Orthologue Macaca mulatta SCAFFOLD126104:4,421-4,426 – AATTAT + ATAATT
ENSMUSG00000043274_OCUN Orthologue Oryctolagus cuniculus scaffold_98029:752-757 – AATTAT + ATAATT
ENSMUSG00000043274_OGAR Orthologue Otolemur garnettii ENSMUSG00000043274_OGAR:134-139 – AAATAT + ATATTT
ENSMUSG00000043274_PCAP Orthologue Procavia capensis ENSMUSG00000043274_PCAP:195-200 – AAATAT + ATATTT
ENSMUSG00000043274_RNOR Orthologue Rattus norvegicus chr3:70,952,551-70,952,556 – AATTAT + ATAATT
ENSMUSG00000043274_TBEL Orthologue Tupaia belangeri ENSMUSG00000043274_TBEL:134-139 – AATTAT + ATAATT
ENSMUSG00000043274_TNIG Orthologue Tetraodon nigroviridis chr16:4,603,371-4,603,376 – AATTAT + ATAATT
ENSMUSG00000043274_XTRO Orthologue Xenopus tropicalis scaffold_10:3,815,992-3,815,997 – AATTAT + ATAATT

Questions or comments: cisred@bcgsc.ca