FILTERS:
pvalue:0.1
Motif craMmus394450
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 craMmus394450
Discovery p-value 2.79E-03
Motif location chr10: 129,214,054-129,214,061 (+) (8 bp)
Search region location chr10: 129,213,711-129,215,646 (+) (1,936 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 16 species: Mus musculus, Bos taurus, Canis familiaris, Dasypus novemcinctus, Echinops telfairi, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Pan troglodytes, Rattus norvegicus, Spermophilus tridecemlineatus, Tupaia belangeri, Xenopus tropicalis
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 5 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (5 annot.): Pax-8(1.31E-04) ,    HNF-1alpha(2.48E-04) ,    Pax-8(2.81E-04) ,    HNF-6(3.04E-04) ,    POU3F2(4.18E-04)
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
45 (Chx10__Pax-8)     63 (HNF-6__POU1F1)     72 (FOXP1a__HNF-1alpha)     134 (HNF-6__MEF-2A)     146 (HNF-1alpha__OCA-B)     194 (POU3F2__Pax-8)     198 (HNF-1alpha__MEF-2A)     215 (HNF-1alpha__YY1)     219 (HNF-1alpha__RSRFC4)     327 (HMG_I__HNF-1alpha)     379 (Evi-1__HNF-1alpha)     488 (HNF-6__POU3F2)     536 (Chx10__HNF-1alpha)     551 (C-EBPdelta__HNF-1alpha)     555 (HNF-6__IRF-1)     618 (HNF-6__OCA-B)     651 (Pax-8__RSRFC4)     661 (POU1F1__Pax-8)     767 (HNF-1alpha__aMEF-2)     782 (Evi-1__Pax-8)     832 (HNF-6__Lhx3a)     1000 (HNF-1alpha__IPF1)     1001 (Pax-8__YY1)     1035 (HNF-6__YY1)     1042 (Chx10__HNF-6)     1047 (HNF-6__RSRFC4)     1106 (HNF-6__aMEF-2)     1118 (HNF-6__IPF1)     1278 (Pax-8__aMEF-2)     1357 (Evi-1__HNF-6)     1411 (HNF-1alpha__Lhx3a)     1417 (IPF1__Pax-8)     1476 (HNF-1alpha__POU3F2)     1489 (HMG_I__HNF-6)     1514 (HNF-1alpha__IRF-1)     1596 (FOXP1a__HNF-6)     1600 (HNF-1alpha__POU1F1)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence TwATGAAT ATTCATsA
Position frequency matrix
1 2 3 4 5 6 7 8
A 5 9 16 0 5 15 16 0
C 0 0 0 0 0 1 0 0
G 0 0 0 0 11 0 0 0
T 11 7 0 16 0 0 0 16
T w A T G A A T
1 2 3 4 5 6 7 8
A 16 0 0 0 16 0 7 11
C 0 0 0 11 0 0 0 0
G 0 0 1 0 0 0 0 0
T 0 16 15 5 0 16 9 5
A T T C A T w 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
ENSMUSG00000057403 Target Mus musculus chr10:129,214,054-129,214,061 + TAATGAAT – ATTCATTA
ENSMUSG00000057403_BTAU Orthologue Bos taurus chr5:35,272,644-35,272,651 + TTATGAAT – ATTCATAA
ENSMUSG00000057403_CFAM Orthologue Canis familiaris chr27:3,058,270-3,058,277 – ATATGAAT + ATTCATAT
ENSMUSG00000057403_DNOV Orthologue Dasypus novemcinctus scaffold_90588:1,958-1,965 – TTATAAAT + ATTTATAA
ENSMUSG00000057403_ETEL Orthologue Echinops telfairi scaffold_291129:51,006-51,013 + TAATGAAT – ATTCATTA
ENSMUSG00000057403_GGAL Orthologue Gallus gallus chr5:2,424,435-2,424,442 – AAATGAAT + ATTCATTT
ENSMUSG00000057403_HSAP Orthologue Homo sapiens chr12:53,976,386-53,976,393 – AAATGAAT + ATTCATTT
ENSMUSG00000057403_LAFR Orthologue Loxodonta africana scaffold_8008:45,571-45,578 – TTATGAAT + ATTCATAA
ENSMUSG00000057403_MDOM Orthologue Monodelphis domestica scaffold_33:18,897,818-18,897,825 + TTATGAAT – ATTCATAA
ENSMUSG00000057403_MMUL Orthologue Macaca mulatta SCAFFOLD70084:150,473-150,480 + TAATGAAT – ATTCATTA
ENSMUSG00000057403_OCUN Orthologue Oryctolagus cuniculus scaffold_93908:1,609-1,616 – TTATAAAT + ATTTATAA
ENSMUSG00000057403_PTRO Orthologue Pan troglodytes chr10:55,236,254-55,236,261 – TTATAAAT + ATTTATAA
ENSMUSG00000057403_RNOR Orthologue Rattus norvegicus chr7:7,051,406-7,051,413 – TAATGCAT + ATGCATTA
ENSMUSG00000057403_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000057403_STRI:177-184 + AAATAAAT – ATTTATTT
ENSMUSG00000057403_TBEL Orthologue Tupaia belangeri ENSMUSG00000057403_TBEL:211-218 + AAATAAAT – ATTTATTT
ENSMUSG00000057403_XTRO Orthologue Xenopus tropicalis scaffold_10:4,550,201-4,550,208 + TAATGAAT – ATTCATTA

Questions or comments: cisred@bcgsc.ca