FILTERS:
pvalue:0.1
Motif craMmus332262
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 craMmus332262
Discovery p-value 2.79E-03
Motif location chr2: 87,260,552-87,260,557 (+) (6 bp)
Search region location chr2: 87,260,197-87,261,965 (+) (1,769 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 16 species: Mus musculus, Canis familiaris, Danio rerio, Erinaceus europaeus, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Myotis lucifugus, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, Procavia capensis, 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 7 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (7 annot.): IPF1(2.90E-04) ,    HNF-1alpha(3.02E-04) ,    POU2F1(3.49E-04) ,    Pax-6(3.53E-04) ,    S8(5.40E-04) ...
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
129 (IPF1__SRY)     139 (OCA-B__POU2F1)     146 (HNF-1alpha__OCA-B)     185 (HNF-1alpha__HNF-3)     199 (IPF1__S8)     274 (IPF1__POU2F1)     275 (HNF-1alpha__SRY)     295 (POU2F1__Pax-6)     322 (HNF-3alpha__POU2F1)     338 (Chx10__IPF1)     358 (Chx10__POU2F1)     375 (HNF-3__POU2F1)     438 (HOXA5__POU2F1)     480 (POU2F1__Pitx2)     522 (POU1F1__POU2F1)     536 (Chx10__HNF-1alpha)     636 (IPF1__POU3F2)     687 (HOXA5__Pax-6)     692 (FOXO4__POU2F1)     706 (AR__POU2F1)     756 (POU2F1__SRY)     774 (HNF-1alpha__POU2F1)     904 (HOXA5__IPF1)     959 (Pax-6__S8)     998 (POU2F1__POU3F2)     1043 (Chx10__Pax-6)     1062 (HNF-1alpha__HOXA5)     1084 (POU1F1__Pax-6)     1115 (AR__HNF-1alpha)     1147 (HNF-1alpha__S8)     1156 (POU3F2__Pax-6)     1180 (POU2F1__POU2F1)     1181 (POU2F1__S8)     1347 (IPF1__OCA-B)     1370 (Pax-6__SRY)     1400 (HNF-3alpha__IPF1)     1426 (HNF-3__IPF1)     1476 (HNF-1alpha__POU3F2)     1524 (OCA-B__Pax-6)     1532 (HNF-1alpha__HNF-3alpha)     1574 (IPF1__POU1F1)     1600 (HNF-1alpha__POU1F1)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence ATCATA TATGAT
Position frequency matrix
1 2 3 4 5 6
A 16 0 0 16 0 16
C 0 0 14 0 0 0
G 0 0 1 0 0 0
T 0 16 1 0 16 0
A T C A T A
1 2 3 4 5 6
A 0 16 0 1 16 0
C 0 0 0 1 0 0
G 0 0 0 14 0 0
T 16 0 16 0 0 16
T A T G A 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
ENSMUSG00000043274 Target Mus musculus chr2:87,260,552-87,260,557 + ATCATA – TATGAT
ENSMUSG00000043274_CFAM Orthologue Canis familiaris chr18:42,958,391-42,958,396 + ATCATA – TATGAT
ENSMUSG00000043274_DRER Orthologue Danio rerio chr10:33,700,809-33,700,814 – ATCATA + TATGAT
ENSMUSG00000043274_EEUR Orthologue Erinaceus europaeus ENSMUSG00000043274_EEUR:204-209 + ATTATA – TATAAT
ENSMUSG00000043274_FRUB Orthologue Fugu rubripes chrUn:304,389,455-304,389,460 – ATCATA + TATGAT
ENSMUSG00000043274_GGAL Orthologue Gallus gallus chr5:58,156-58,161 + ATCATA – TATGAT
ENSMUSG00000043274_HSAP Orthologue Homo sapiens chr11:55,492,408-55,492,413 – ATCATA + TATGAT
ENSMUSG00000043274_LAFR Orthologue Loxodonta africana scaffold_28824:1,096-1,101 – ATCATA + TATGAT
ENSMUSG00000043274_MDOM Orthologue Monodelphis domestica scaffold_33:17,446,295-17,446,300 – ATCATA + TATGAT
ENSMUSG00000043274_MLUC Orthologue Myotis lucifugus ENSMUSG00000043274_MLUC:237-242 + ATCATA – TATGAT
ENSMUSG00000043274_MMUL Orthologue Macaca mulatta SCAFFOLD126104:4,516-4,521 + ATGATA – TATCAT
ENSMUSG00000043274_OCUN Orthologue Oryctolagus cuniculus scaffold_98029:18-23 + ATCATA – TATGAT
ENSMUSG00000043274_OGAR Orthologue Otolemur garnettii ENSMUSG00000043274_OGAR:176-181 + ATCATA – TATGAT
ENSMUSG00000043274_PCAP Orthologue Procavia capensis ENSMUSG00000043274_PCAP:77-82 + ATCATA – TATGAT
ENSMUSG00000043274_PTRO Orthologue Pan troglodytes 9_random:27,135,554-27,135,559 – ATCATA + TATGAT
ENSMUSG00000043274_RNOR Orthologue Rattus norvegicus chr3:70,952,453-70,952,458 + ATCATA – TATGAT

Questions or comments: cisred@bcgsc.ca