FILTERS:
pvalue:0.1
Motif craMmus394978
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 craMmus394978
Discovery p-value 2.79E-03
Motif location chr8: 107,852,574-107,852,579 (-) (6 bp)
Search region location chr8: 107,851,457-107,853,184 (-) (1,728 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 23 species: Mus musculus, Bos taurus, Canis familiaris, Danio rerio, Echinops telfairi, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Myotis lucifugus, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, Procavia capensis, Pongo pygmaeus, Pan troglodytes, Rattus norvegicus, Sorex araneus, Spermophilus tridecemlineatus, Tupaia belangeri, Tetraodon nigroviridis, Xenopus tropicalis
Found with
'De Novo' motif group ID This motif was not submitted for clustering.
Similar to
(annotation p-value)		 There are 10 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (8 annot.): POU2F1(6.48E-06) ,    POU2F1(2.11E-05) ,    OCA-B(4.39E-05) ,    POU2F1(4.64E-05) ,    Hlf(5.91E-05) ...
ORegAnno: (2 annot.): FoxA1(3.06E-04) ,    FoxA1(9.28E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
40 (Hlf__POU1F1)     85 (OCA-B__POU1F1)     139 (OCA-B__POU2F1)     147 (AFP1__POU3F2)     160 (POU1F1__POU3F2)     194 (POU3F2__Pax-8)     202 (Chx10__OCA-B)     252 (POU3F2__POU3F2)     295 (POU2F1__Pax-6)     358 (Chx10__POU2F1)     362 (OCA-B__POU3F2)     488 (HNF-6__POU3F2)     522 (POU1F1__POU2F1)     618 (HNF-6__OCA-B)     697 (HNF-6__Hlf)     751 (AFP1__POU2F1)     759 (HNF-6__POU2F1)     792 (AFP1__OCA-B)     819 (OCA-B__POU6F1_(c2))     849 (C-EBPbeta__POU2F1)     888 (Hlf__OCA-B)     922 (FOXJ2__POU2F1)     933 (C-EBPbeta__OCA-B)     942 (POU2F1__POU6F1_(c2))     998 (POU2F1__POU3F2)     1008 (POU2F1__Pax-8)     1127 (IRF-1__POU2F1)     1156 (POU3F2__Pax-6)     1159 (Hlf__POU2F1)     1180 (POU2F1__POU2F1)     1232 (IRF-1__OCA-B)     1233 (FOXJ2__POU3F2)     1336 (POU3F2__POU6F1_(c2))     1382 (Hlf__POU3F2)     1431 (FOXJ2__Hlf)     1432 (OCA-B__OCA-B)     1433 (FOXJ2__OCA-B)     1442 (Chx10__POU3F2)     1524 (OCA-B__Pax-6)     1530 (Hlf__POU6F1_(c2))     1554 (C-EBPbeta__POU3F2)     1578 (IRF-1__POU3F2)     1580 (Chx10__Hlf)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence ATGCAA TTGCAT
Position frequency matrix
1 2 3 4 5 6
A 23 0 0 0 23 23
C 0 0 0 23 0 0
G 0 0 23 0 0 0
T 0 23 0 0 0 0
A T G C A A
1 2 3 4 5 6
A 0 0 0 0 23 0
C 0 0 0 23 0 0
G 0 0 23 0 0 0
T 23 23 0 0 0 23
T T G C 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
ENSMUSG00000057387 Target Mus musculus chr8:107,852,574-107,852,579 + ATGCAA – TTGCAT
ENSMUSG00000057387_BTAU Orthologue Bos taurus chr18:34,030,674-34,030,679 – ATGCAA + TTGCAT
ENSMUSG00000057387_CFAM Orthologue Canis familiaris chr5:81,161,753-81,161,758 + ATGCAA – TTGCAT
ENSMUSG00000057387_DRER Orthologue Danio rerio chr7:55,215,587-55,215,592 + ATGCAA – TTGCAT
ENSMUSG00000057387_ETEL Orthologue Echinops telfairi scaffold_293253:6,569-6,574 – ATGCAA + TTGCAT
ENSMUSG00000057387_FRUB Orthologue Fugu rubripes chrUn:148,194,151-148,194,156 – ATGCAA + TTGCAT
ENSMUSG00000057387_GGAL Orthologue Gallus gallus 11_random:838,773-838,778 – ATGCAA + TTGCAT
ENSMUSG00000057387_HSAP Orthologue Homo sapiens chr16:71,016,300-71,016,305 + ATGCAA – TTGCAT
ENSMUSG00000057387_LAFR Orthologue Loxodonta africana scaffold_24594:10,285-10,290 + ATGCAA – TTGCAT
ENSMUSG00000057387_MDOM Orthologue Monodelphis domestica scaffold_23:2,076,808-2,076,813 + ATGCAA – TTGCAT
ENSMUSG00000057387_MLUC Orthologue Myotis lucifugus ENSMUSG00000057387_MLUC:470-475 + ATGCAA – TTGCAT
ENSMUSG00000057387_MMUL Orthologue Macaca mulatta SCAFFOLD65106:68,955-68,960 + ATGCAA – TTGCAT
ENSMUSG00000057387_OCUN Orthologue Oryctolagus cuniculus scaffold_210420:48,538-48,543 – ATGCAA + TTGCAT
ENSMUSG00000057387_OGAR Orthologue Otolemur garnettii ENSMUSG00000057387_OGAR:250-255 + ATGCAA – TTGCAT
ENSMUSG00000057387_PCAP Orthologue Procavia capensis ENSMUSG00000057387_PCAP:614-619 + ATGCAA – TTGCAT
ENSMUSG00000057387_PPYG Orthologue Pongo pygmaeus ENSMUSG00000057387_PPYG:249-254 + ATGCAA – TTGCAT
ENSMUSG00000057387_PTRO Orthologue Pan troglodytes chr18:65,386,943-65,386,948 + ATGCAA – TTGCAT
ENSMUSG00000057387_RNOR Orthologue Rattus norvegicus chr19:39,117,247-39,117,252 – ATGCAA + TTGCAT
ENSMUSG00000057387_SARA Orthologue Sorex araneus ENSMUSG00000057387_SARA:236-241 + ATGCAA – TTGCAT
ENSMUSG00000057387_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000057387_STRI:1,383-1,388 + ATGCAA – TTGCAT
ENSMUSG00000057387_TBEL Orthologue Tupaia belangeri ENSMUSG00000057387_TBEL:365-370 + ATGCAA – TTGCAT
ENSMUSG00000057387_TNIG Orthologue Tetraodon nigroviridis chr5:5,949,439-5,949,444 – ATGCAA + TTGCAT
ENSMUSG00000057387_XTRO Orthologue Xenopus tropicalis scaffold_13:3,792,464-3,792,469 + ATGCAA – TTGCAT

Questions or comments: cisred@bcgsc.ca