FILTERS:
pvalue:0.1
Motif craMmus355250
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 craMmus355250
Discovery p-value 2.79E-03
Motif location chr13: 63,009,665-63,009,672 (+) (8 bp)
Search region location chr13: 63,008,192-63,009,964 (+) (1,773 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 17 species: Mus musculus, Choloepus hoffmanni, Cavia porcellus, Dasypus novemcinctus, Danio rerio, Equus caballus, Erinaceus europaeus, Echinops telfairi, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, Rattus norvegicus, Xenopus tropicalis
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 12 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (10 annot.): Nkx2-2(1.08E-04) ,    E4BP4(1.30E-04) ,    Nkx3-1(1.43E-04) ,    HNF-1alpha(1.61E-04) ,    Hlf(2.10E-04) ...
ORegAnno: (2 annot.): FoxA1(3.76E-04) ,    FoxA1(3.76E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
118 (Chx10__Evi-1)     215 (HNF-1alpha__YY1)     261 (Chx10__E4BP4)     272 (Hlf__Nkx6-2)     287 (C-EBPdelta__POU2F1)     337 (Nkx3-1__YY1)     358 (Chx10__POU2F1)     379 (Evi-1__HNF-1alpha)     388 (E4BP4__POU2F1)     464 (Evi-1__S8)     512 (Evi-1__Hlf)     525 (AFP1__Chx10)     536 (Chx10__HNF-1alpha)     574 (Pax-2__S8)     578 (E4BP4__Nkx6-2)     602 (HNF-1alpha__Nkx6-2)     707 (Chx10__S8)     752 (HNF-1alpha__Pax-2)     774 (HNF-1alpha__POU2F1)     826 (Chx10__YY1)     870 (E4BP4__YY1)     894 (Nkx2-2__POU2F1)     911 (S8__YY1)     963 (Evi-1__Nkx3-1)     1010 (Chx10__Nkx3-1)     1013 (Nkx6-2__S8)     1059 (AFP1__Nkx3-1)     1132 (Chx10__Pax-2)     1155 (E4BP4__Evi-1)     1159 (Hlf__POU2F1)     1161 (Chx10__Nkx2-2)     1181 (POU2F1__S8)     1287 (Nkx3-1__Nkx6-2)     1394 (Chx10__Chx10)     1395 (AFP1__S8)     1420 (Nkx3-1__POU2F1)     1559 (Chx10__Nkx6-2)     1572 (AFP1__HNF-1alpha)     1580 (Chx10__Hlf)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence rTTAATTA TAATTAAy
Position frequency matrix
1 2 3 4 5 6 7 8
A 8 0 5 17 11 0 0 12
C 0 0 0 0 5 0 0 0
G 9 0 0 0 0 0 0 0
T 0 17 12 0 1 17 17 5
r T T A A T T A
1 2 3 4 5 6 7 8
A 5 17 17 1 0 12 17 0
C 0 0 0 0 0 0 0 9
G 0 0 0 5 0 0 0 0
T 12 0 0 11 17 5 0 8
T A A T T A A y

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
ENSMUSG00000051466 Target Mus musculus chr13:63,009,665-63,009,672 + ATTACTTA – TAAGTAAT
ENSMUSG00000051466_CHOF Orthologue Choloepus hoffmanni ENSMUSG00000051466_CHOF:126-133 – ATAAATTA + TAATTTAT
ENSMUSG00000051466_CPOR Orthologue Cavia porcellus ENSMUSG00000051466_CPOR:95-102 – GTTAATTT + AAATTAAC
ENSMUSG00000051466_DNOV Orthologue Dasypus novemcinctus scaffold_19302:19,822-19,829 + GTTAATTA – TAATTAAC
ENSMUSG00000051466_DRER Orthologue Danio rerio chr10:33,720,397-33,720,404 + GTAATTTA – TAAATTAC
ENSMUSG00000051466_ECAB Orthologue Equus caballus ENSMUSG00000051466_ECAB:4-11 + ATTAATTT – AAATTAAT
ENSMUSG00000051466_EEUR Orthologue Erinaceus europaeus ENSMUSG00000051466_EEUR:145-152 – GTTAATTT + AAATTAAC
ENSMUSG00000051466_ETEL Orthologue Echinops telfairi scaffold_206473:2,520-2,527 – GTTACTTT + AAAGTAAC
ENSMUSG00000051466_GGAL Orthologue Gallus gallus chr5:56,820-56,827 – ATAAATTA + TAATTTAT
ENSMUSG00000051466_HSAP Orthologue Homo sapiens chr1:244,108,884-244,108,891 – ATTAATTA + TAATTAAT
ENSMUSG00000051466_LAFR Orthologue Loxodonta africana scaffold_156204:2,094-2,101 + GTAAATTA – TAATTTAC
ENSMUSG00000051466_MDOM Orthologue Monodelphis domestica scaffold_33:17,532,562-17,532,569 + GTTACTTT – AAAGTAAC
ENSMUSG00000051466_MMUL Orthologue Macaca mulatta SCAFFOLD478:4,733-4,740 – ATAAATTA + TAATTTAT
ENSMUSG00000051466_OCUN Orthologue Oryctolagus cuniculus scaffold_162932:2,904-2,911 + GTTAATTA – TAATTAAC
ENSMUSG00000051466_OGAR Orthologue Otolemur garnettii ENSMUSG00000051466_OGAR:247-254 – GTTAATTA + TAATTAAC
ENSMUSG00000051466_RNOR Orthologue Rattus norvegicus chr17:5,520,390-5,520,397 – ATTACTTA + TAAGTAAT
ENSMUSG00000051466_XTRO Orthologue Xenopus tropicalis scaffold_786:498,024-498,031 + ATTACTTA – TAAGTAAT

Questions or comments: cisred@bcgsc.ca