FILTERS:
pvalue:0.1
Motif craMmus304434
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 craMmus304434
Discovery p-value 2.79E-03
Motif location chr2: 87,111,556-87,111,565 (+) (10 bp)
Search region location chr2: 87,111,062-87,112,761 (+) (1,700 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 19 species: Mus musculus, Bos taurus, Canis familiaris, Dasypus novemcinctus, Danio rerio, Echinops telfairi, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Ornithorhynchus anatinus, Otolemur garnettii, Procavia capensis, Pan troglodytes, Rattus norvegicus, 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 6 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (3 annot.): S8(6.39E-05) ,    Chx10(2.35E-04) ,    HOXA5(9.91E-04)
ORegAnno: (3 annot.): FoxA1(3.00E-05) ,    FoxA1(3.00E-05) ,    FoxA1(4.25E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
199 (IPF1__S8)     226 (POU3F2__S8)     254 (Cdx-2__Chx10)     265 (Chx10__MEF-2A)     338 (Chx10__IPF1)     339 (HOXA5__S8)     358 (Chx10__POU2F1)     392 (FOXP1a__S8)     431 (Crx__S8)     498 (Chx10__HOXA5)     525 (AFP1__Chx10)     536 (Chx10__HNF-1alpha)     601 (IRF-7A__S8)     635 (Chx10__Nkx2-5)     639 (Chx10__Crx)     707 (Chx10__S8)     746 (Chx10__MRF-2)     764 (Cdx-2__S8)     863 (MRF-2__S8)     956 (Chx10__IRF-7A)     1013 (Nkx6-2__S8)     1042 (Chx10__HNF-6)     1064 (Chx10__FOXP1a)     1147 (HNF-1alpha__S8)     1181 (POU2F1__S8)     1207 (Chx10__IRF-1)     1224 (C-EBPbeta__Chx10)     1337 (IRF-1__S8)     1374 (HNF-6__S8)     1394 (Chx10__Chx10)     1395 (AFP1__S8)     1429 (Chx10__RSRFC4)     1442 (Chx10__POU3F2)     1450 (S8__aMEF-2)     1452 (RSRFC4__S8)     1471 (Chx10__aMEF-2)     1508 (C-EBPbeta__S8)     1559 (Chx10__Nkx6-2)     1601 (MEF-2A__S8)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence wAATTrATwA TsATyAATTs
Position frequency matrix
1 2 3 4 5 6 7 8 9 10
A 10 13 17 1 0 12 14 0 7 14
C 0 0 0 0 0 0 5 0 0 0
G 0 0 0 0 0 7 0 0 0 0
T 9 6 2 18 19 0 0 19 12 5
w A A T T n A T n A
1 2 3 4 5 6 7 8 9 10
A 5 12 19 0 0 19 18 2 6 9
C 0 0 0 0 7 0 0 0 0 0
G 0 0 0 5 0 0 0 0 0 0
T 14 7 0 14 12 0 1 17 13 10
T n A T n A A T T 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
ENSMUSG00000070855 Target Mus musculus chr2:87,111,556-87,111,565 + TAATTACTTA – TAAGTAATTA
ENSMUSG00000070855_BTAU Orthologue Bos taurus chr2:605,925-605,934 – TAATTGCTTA + TAAGCAATTA
ENSMUSG00000070855_CFAM Orthologue Canis familiaris chr18:42,949,073-42,949,082 – AAATTACTAA + TTAGTAATTT
ENSMUSG00000070855_DNOV Orthologue Dasypus novemcinctus scaffold_56908:322-331 + TAATTGATTA – TAATCAATTA
ENSMUSG00000070855_DRER Orthologue Danio rerio chr15:36,016,788-36,016,797 + TATTTAATTA – TAATTAAATA
ENSMUSG00000070855_ETEL Orthologue Echinops telfairi scaffold_240389:10,834-10,843 – TAATTGATTA + TAATCAATTA
ENSMUSG00000070855_FRUB Orthologue Fugu rubripes chrUn:304,389,177-304,389,186 + ATATTGATTA – TAATCAATAT
ENSMUSG00000070855_GGAL Orthologue Gallus gallus chr5:2,401,065-2,401,074 + TAATTAATAT – ATATTAATTA
ENSMUSG00000070855_HSAP Orthologue Homo sapiens chr11:55,493,822-55,493,831 + TAATTAATTT – AAATTAATTA
ENSMUSG00000070855_LAFR Orthologue Loxodonta africana scaffold_8581:46,887-46,896 + ATATTAATTA – TAATTAATAT
ENSMUSG00000070855_MDOM Orthologue Monodelphis domestica scaffold_33:17,709,135-17,709,144 + ATATTAATAA – TTATTAATAT
ENSMUSG00000070855_MMUL Orthologue Macaca mulatta SCAFFOLD126104:4,771-4,780 – ATATTAATTA + TAATTAATAT
ENSMUSG00000070855_OANA Orthologue Ornithorhynchus anatinus ENSMUSG00000070855_OANA:255-264 – AAAATGATTA + TAATCATTTT
ENSMUSG00000070855_OGAR Orthologue Otolemur garnettii ENSMUSG00000070855_OGAR:553-562 – AATTTGATTT + AAATCAAATT
ENSMUSG00000070855_PCAP Orthologue Procavia capensis ENSMUSG00000070855_PCAP:263-272 – AAATTAATAA + TTATTAATTT
ENSMUSG00000070855_PTRO Orthologue Pan troglodytes 9_random:27,135,493-27,135,502 + AAATTGCTAA – TTAGCAATTT
ENSMUSG00000070855_RNOR Orthologue Rattus norvegicus chr3:70,832,097-70,832,106 – TTATTACTAA + TTAGTAATAA
ENSMUSG00000070855_TNIG Orthologue Tetraodon nigroviridis chr16:4,609,812-4,609,821 – AAATTAATTT + AAATTAATTT
ENSMUSG00000070855_XTRO Orthologue Xenopus tropicalis scaffold_10:3,724,687-3,724,696 – TTATTAATAT + ATATTAATAA

Questions or comments: cisred@bcgsc.ca