FILTERS:
pvalue:0.1
Motif craMmus394470
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 craMmus394470
Discovery p-value 2.79E-03
Motif location chr8: 107,852,628-107,852,641 (-) (14 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, Canis familiaris, Cavia porcellus, Danio rerio, Equus caballus, Erinaceus europaeus, Echinops telfairi, 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 7 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (7 annot.): POU6F1_(c2)(1.88E-05) ,    AFP1(3.31E-05) ,    POU1F1(4.53E-05) ,    Chx10(3.60E-04) ,    Pbx(5.37E-04) ...
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
40 (Hlf__POU1F1)     45 (Chx10__Pax-8)     85 (OCA-B__POU1F1)     147 (AFP1__POU3F2)     160 (POU1F1__POU3F2)     202 (Chx10__OCA-B)     314 (AFP1__FOXJ2)     358 (Chx10__POU2F1)     384 (Chx10__FOXJ2)     412 (AFP1__IRF-1)     522 (POU1F1__POU2F1)     525 (AFP1__Chx10)     546 (AFP1__Pax-6)     611 (Chx10__POU1F1)     661 (POU1F1__Pax-8)     751 (AFP1__POU2F1)     772 (POU6F1_(c2)__Pax-6)     792 (AFP1__OCA-B)     819 (OCA-B__POU6F1_(c2))     843 (C-EBPbeta__POU6F1_(c2))     914 (Chx10__POU6F1_(c2))     942 (POU2F1__POU6F1_(c2))     1016 (FOXJ2__POU6F1_(c2))     1043 (Chx10__Pax-6)     1084 (POU1F1__Pax-6)     1110 (FOXJ2__POU1F1)     1207 (Chx10__IRF-1)     1224 (C-EBPbeta__Chx10)     1263 (POU6F1_(c2)__Pax-8)     1285 (IRF-1__POU1F1)     1302 (C-EBPbeta__POU1F1)     1336 (POU3F2__POU6F1_(c2))     1394 (Chx10__Chx10)     1442 (Chx10__POU3F2)     1530 (Hlf__POU6F1_(c2))     1580 (Chx10__Hlf)     1599 (IRF-1__POU6F1_(c2))    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence TGTATAATTTATGA TCATAAATTATACA
Position frequency matrix
1 2 3 4 5 6 7 8 9 10 11 12 13 14
A 0 3 0 23 3 19 16 0 5 0 17 0 0 20
C 0 2 0 0 0 0 0 0 0 2 0 0 1 1
G 0 18 0 0 0 4 0 0 0 0 6 4 21 2
T 23 0 23 0 20 0 7 23 18 21 0 19 1 0
T G T A T A A T T T A T G A
1 2 3 4 5 6 7 8 9 10 11 12 13 14
A 0 1 19 0 21 18 23 7 0 20 0 23 0 23
C 2 21 4 6 0 0 0 0 4 0 0 0 18 0
G 1 1 0 0 2 0 0 0 0 0 0 0 2 0
T 20 0 0 17 0 5 0 16 19 3 23 0 3 0
T C A T A A A T T A T A C 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
ENSMUSG00000057387 Target Mus musculus chr8:107,852,628-107,852,641 + TGTATAATTTATGA – TCATAAATTATACA
ENSMUSG00000057387_CFAM Orthologue Canis familiaris chr5:81,161,708-81,161,721 – TGTATAATTTATGA + TCATAAATTATACA
ENSMUSG00000057387_CPOR Orthologue Cavia porcellus ENSMUSG00000057387_CPOR:231-244 – TGTATAATTTATGA + TCATAAATTATACA
ENSMUSG00000057387_DRER Orthologue Danio rerio chr7:55,216,016-55,216,029 + TGTATGTTTTAGCC – GGCTAAAACATACA
ENSMUSG00000057387_ECAB Orthologue Equus caballus ENSMUSG00000057387_ECAB:36-49 – TCTATATTTTGTTA + TAACAAAATATAGA
ENSMUSG00000057387_EEUR Orthologue Erinaceus europaeus ENSMUSG00000057387_EEUR:398-411 + TATATGTTACGGGG – CCCCGTAACATATA
ENSMUSG00000057387_ETEL Orthologue Echinops telfairi scaffold_293253:7,089-7,102 + TGTATAATTTATGA – TCATAAATTATACA
ENSMUSG00000057387_HSAP Orthologue Homo sapiens chr16:71,016,255-71,016,268 – TGTATAATTTATGA + TCATAAATTATACA
ENSMUSG00000057387_LAFR Orthologue Loxodonta africana scaffold_24594:10,240-10,253 – TGTATAATTTATGA + TCATAAATTATACA
ENSMUSG00000057387_MDOM Orthologue Monodelphis domestica scaffold_23:2,076,763-2,076,776 – TGTATAATTTATGA + TCATAAATTATACA
ENSMUSG00000057387_MLUC Orthologue Myotis lucifugus ENSMUSG00000057387_MLUC:446-459 + TATATGTTACGGGG – CCCCGTAACATATA
ENSMUSG00000057387_MMUL Orthologue Macaca mulatta SCAFFOLD65106:68,910-68,923 – TGTATAATTTATGA + TCATAAATTATACA
ENSMUSG00000057387_OCUN Orthologue Oryctolagus cuniculus scaffold_210420:48,575-48,588 + TGTATAATTTATGA – TCATAAATTATACA
ENSMUSG00000057387_OGAR Orthologue Otolemur garnettii ENSMUSG00000057387_OGAR:205-218 – TGTATAATTTATGA + TCATAAATTATACA
ENSMUSG00000057387_PCAP Orthologue Procavia capensis ENSMUSG00000057387_PCAP:569-582 – TGTATAATTTATGA + TCATAAATTATACA
ENSMUSG00000057387_PPYG Orthologue Pongo pygmaeus ENSMUSG00000057387_PPYG:204-217 – TGTATAATTTATGA + TCATAAATTATACA
ENSMUSG00000057387_PTRO Orthologue Pan troglodytes chr18:65,386,898-65,386,911 – TGTATAATTTATGA + TCATAAATTATACA
ENSMUSG00000057387_RNOR Orthologue Rattus norvegicus chr19:39,117,284-39,117,297 + TGTATAATTTATGA – TCATAAATTATACA
ENSMUSG00000057387_SARA Orthologue Sorex araneus ENSMUSG00000057387_SARA:152-165 + TGTAAATTATGTGA – TCACATAATTTACA
ENSMUSG00000057387_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000057387_STRI:407-420 – TGTATAATTTATGA + TCATAAATTATACA
ENSMUSG00000057387_TBEL Orthologue Tupaia belangeri ENSMUSG00000057387_TBEL:281-294 + TGTAAATTATGTGA – TCACATAATTTACA
ENSMUSG00000057387_TNIG Orthologue Tetraodon nigroviridis chr5:5,948,659-5,948,672 – TATAAGTTATGGGA + TCCCATAACTTATA
ENSMUSG00000057387_XTRO Orthologue Xenopus tropicalis scaffold_13:3,792,419-3,792,432 – TCTATAATTTATGA + TCATAAATTATAGA

Questions or comments: cisred@bcgsc.ca