FILTERS:
pvalue:0.1
Motif craMmus336858
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 craMmus336858
Discovery p-value 2.79E-03
Motif location chr2: 87,867,914-87,867,921 (+) (8 bp)
Search region location chr2: 87,866,875-87,868,639 (+) (1,765 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 17 species: Mus musculus, Canis familiaris, Cavia porcellus, Dasypus novemcinctus, Danio rerio, Erinaceus europaeus, Echinops telfairi, Fugu rubripes, Gallus gallus, Loxodonta africana, Monodelphis domestica, Oryctolagus cuniculus, Otolemur garnettii, Procavia capensis, Pan troglodytes, Rattus norvegicus, Tetraodon nigroviridis
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 8 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (7 annot.): HOXA5(1.69E-04) ,    HNF-1alpha(3.48E-04) ,    IPF1(3.77E-04) ,    POU1F1(5.16E-04) ,    Lhx3a(5.52E-04) ...
ORegAnno: (1 annot.): FoxA1(9.28E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
26 (HOXA5__Sox5)     39 (Cdx-2__HOXA5)     60 (Cdx-2__HNF-1alpha)     72 (FOXP1a__HNF-1alpha)     74 (IPF1__TEF)     97 (HNF-1alpha__TEF)     120 (IPF1__Sox5)     151 (IPF1__aMEF-2)     161 (Brachyury__HOXA5)     199 (IPF1__S8)     219 (HNF-1alpha__RSRFC4)     228 (IPF1__IPF1)     289 (IPF1__Lhx3a)     338 (Chx10__IPF1)     339 (HOXA5__S8)     361 (HOXA5__POU3F2)     371 (Brachyury__HNF-1alpha)     379 (Evi-1__HNF-1alpha)     465 (HOXA5__RSRFC4)     477 (HOXA5__POU1F1)     498 (Chx10__HOXA5)     514 (AIRE__HOXA5)     536 (Chx10__HNF-1alpha)     636 (IPF1__POU3F2)     767 (HNF-1alpha__aMEF-2)     856 (Cdx-2__IPF1)     904 (HOXA5__IPF1)     1000 (HNF-1alpha__IPF1)     1025 (HOXA5__Lhx3a)     1038 (IPF1__RSRFC4)     1062 (HNF-1alpha__HOXA5)     1135 (HOXA5__TEF)     1147 (HNF-1alpha__S8)     1197 (HNF-1alpha__Sox5)     1221 (Evi-1__IPF1)     1254 (HNF-1alpha__HNF-1alpha)     1411 (HNF-1alpha__Lhx3a)     1412 (FOXP1a__HOXA5)     1439 (Evi-1__HOXA5)     1464 (HOXA5__aMEF-2)     1476 (HNF-1alpha__POU3F2)     1506 (AIRE__IPF1)     1512 (AIRE__HNF-1alpha)     1569 (FOXP1a__IPF1)     1574 (IPF1__POU1F1)     1593 (Brachyury__IPF1)     1600 (HNF-1alpha__POU1F1)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence AAAATTAA TTAATTTT
Position frequency matrix
1 2 3 4 5 6 7 8
A 15 17 17 17 0 0 16 17
C 0 0 0 0 0 3 0 0
G 0 0 0 0 0 0 0 0
T 2 0 0 0 17 14 1 0
A A A A T T A A
1 2 3 4 5 6 7 8
A 0 1 14 17 0 0 0 2
C 0 0 0 0 0 0 0 0
G 0 0 3 0 0 0 0 0
T 17 16 0 0 17 17 17 15
T T A A T T 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
ENSMUSG00000045150 Target Mus musculus chr2:87,867,914-87,867,921 + AAAATTAA – TTAATTTT
ENSMUSG00000045150_CFAM Orthologue Canis familiaris chr18:43,169,999-43,170,006 – AAAATTAA + TTAATTTT
ENSMUSG00000045150_CPOR Orthologue Cavia porcellus ENSMUSG00000045150_CPOR:156-163 + AAAATTAA – TTAATTTT
ENSMUSG00000045150_DNOV Orthologue Dasypus novemcinctus scaffold_22184:9,842-9,849 – AAAATTAA + TTAATTTT
ENSMUSG00000045150_DRER Orthologue Danio rerio chr10:33,719,816-33,719,823 + AAAATTAA – TTAATTTT
ENSMUSG00000045150_EEUR Orthologue Erinaceus europaeus ENSMUSG00000045150_EEUR:9-16 + AAAATTAA – TTAATTTT
ENSMUSG00000045150_ETEL Orthologue Echinops telfairi scaffold_272748:12,770-12,777 – AAAATCAA + TTGATTTT
ENSMUSG00000045150_FRUB Orthologue Fugu rubripes chrUn:265,457,346-265,457,353 – AAAATCAA + TTGATTTT
ENSMUSG00000045150_GGAL Orthologue Gallus gallus chr5:2,428,891-2,428,898 + AAAATTAA – TTAATTTT
ENSMUSG00000045150_LAFR Orthologue Loxodonta africana scaffold_8:263,709-263,716 – AAAATTAA + TTAATTTT
ENSMUSG00000045150_MDOM Orthologue Monodelphis domestica scaffold_33:17,123,341-17,123,348 + AAAATTAA – TTAATTTT
ENSMUSG00000045150_OCUN Orthologue Oryctolagus cuniculus scaffold_212637:2,068-2,075 – AAAATTAA + TTAATTTT
ENSMUSG00000045150_OGAR Orthologue Otolemur garnettii ENSMUSG00000045150_OGAR:18-25 – AAAATTAA + TTAATTTT
ENSMUSG00000045150_PCAP Orthologue Procavia capensis ENSMUSG00000045150_PCAP:968-975 + AAAATTAA – TTAATTTT
ENSMUSG00000045150_PTRO Orthologue Pan troglodytes chr9:56,243,736-56,243,743 – TAAATTAA + TTAATTTA
ENSMUSG00000045150_RNOR Orthologue Rattus norvegicus chr3:71,662,435-71,662,442 + TAAATTTA – TAAATTTA
ENSMUSG00000045150_TNIG Orthologue Tetraodon nigroviridis chr2:14,429,010-14,429,017 – AAAATCAA + TTGATTTT

Questions or comments: cisred@bcgsc.ca