FILTERS:
pvalue:0.1
Motif craMmus263984
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 craMmus263984
Discovery p-value 2.79E-03
Motif location chr2: 87,589,093-87,589,100 (+) (8 bp)
Search region location chr2: 87,588,385-87,590,113 (+) (1,729 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 14 species: Mus musculus, Bos taurus, Canis familiaris, Callithrix jacchus, Dasypus novemcinctus, Danio rerio, Echinops telfairi, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Pan troglodytes, Rattus norvegicus
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: (3 annot.): HNF-1alpha(1.75E-04) ,    CUTL1(2.93E-04) ,    FOXP1a(5.96E-04)
ORegAnno: (2 annot.): FoxA1(2.70E-04) ,    FoxA1(4.08E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
15 (COMP1__HNF-1alpha)     29 (C-EBPgamma__HNF-1alpha)     31 (CUTL1__POU6F1_(c2))     50 (HNF-1alpha__HNF-6)     62 (COMP1__CUTL1)     164 (HNF-1alpha__SRF)     180 (CUTL1__HOXA5)     185 (HNF-1alpha__HNF-3)     203 (CUTL1__Nkx3-1)     285 (HNF-1alpha__POU6F1_(c2))     329 (CUTL1__Chx10)     332 (CUTL1__HNF-6)     347 (CUTL1__Pax-8)     387 (CUTL1__IPF1)     391 (CUTL1__POU3F2)     393 (CUTL1__POU2F1)     536 (Chx10__HNF-1alpha)     543 (E4BP4__HNF-1alpha)     545 (CUTL1__HNF-3)     774 (HNF-1alpha__POU2F1)     846 (FOXD3__HNF-1alpha)     940 (HNF-1alpha__Nkx3-1)     968 (HNF-1alpha__Pax-8)     1000 (HNF-1alpha__IPF1)     1062 (HNF-1alpha__HOXA5)     1165 (CUTL1__FOXD3)     1455 (CUTL1__SRF)     1476 (HNF-1alpha__POU3F2)     1548 (C-EBPgamma__CUTL1)     1563 (CUTL1__E4BP4)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence AATTyATA TATrAATT
Position frequency matrix
1 2 3 4 5 6 7 8
A 14 13 0 4 0 14 0 14
C 0 0 0 0 6 0 0 0
G 0 0 0 0 0 0 0 0
T 0 1 14 10 8 0 14 0
A A T T y A T A
1 2 3 4 5 6 7 8
A 0 14 0 8 10 14 1 0
C 0 0 0 0 0 0 0 0
G 0 0 0 6 0 0 0 0
T 14 0 14 0 4 0 13 14
T A T r 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
ENSMUSG00000068817 Target Mus musculus chr2:87,589,093-87,589,100 + AATTCATA – TATGAATT
ENSMUSG00000068817_BTAU Orthologue Bos taurus chr1:22,331,118-22,331,125 + AATTCATA – TATGAATT
ENSMUSG00000068817_CFAM Orthologue Canis familiaris chr18:43,090,959-43,090,966 – AATTTATA + TATAAATT
ENSMUSG00000068817_CJAC Orthologue Callithrix jacchus ENSMUSG00000068817_CJAC:332-339 + ATTTCATA – TATGAAAT
ENSMUSG00000068817_DNOV Orthologue Dasypus novemcinctus scaffold_18954:4,178-4,185 + AATTTATA – TATAAATT
ENSMUSG00000068817_DRER Orthologue Danio rerio chr15:36,003,635-36,003,642 – AATATATA + TATATATT
ENSMUSG00000068817_ETEL Orthologue Echinops telfairi scaffold_293493:56,950-56,957 – AATTTATA + TATAAATT
ENSMUSG00000068817_GGAL Orthologue Gallus gallus chr5:2,424,600-2,424,607 – AATTTATA + TATAAATT
ENSMUSG00000068817_HSAP Orthologue Homo sapiens chr11:55,439,399-55,439,406 + AATATATA – TATATATT
ENSMUSG00000068817_LAFR Orthologue Loxodonta africana scaffold_28740:33,374-33,381 – AATTCATA + TATGAATT
ENSMUSG00000068817_MDOM Orthologue Monodelphis domestica scaffold_33:17,149,397-17,149,404 + AATACATA – TATGTATT
ENSMUSG00000068817_MMUL Orthologue Macaca mulatta SCAFFOLD115116:157,008-157,015 – AATTTATA + TATAAATT
ENSMUSG00000068817_PTRO Orthologue Pan troglodytes 9_random:27,082,219-27,082,226 + AATATATA – TATATATT
ENSMUSG00000068817_RNOR Orthologue Rattus norvegicus chr3:71,428,175-71,428,182 – AATTCATA + TATGAATT

Questions or comments: cisred@bcgsc.ca