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pvalue:0.1
Motif craMmus214887
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 craMmus214887
Discovery p-value 2.79E-03
Motif location chr1: 110,854,714-110,854,725 (-) (12 bp)
Search region location chr1: 110,854,096-110,856,980 (-) (2,885 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 14 species: Mus musculus, Canis familiaris, Callithrix jacchus, Echinops telfairi, Gallus gallus, Homo sapiens, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Pongo pygmaeus, Pan troglodytes, Rattus norvegicus, 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 5 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (5 annot.): POU3F2(1.87E-05) ,    POU6F1_(c2)(1.47E-04) ,    Evi-1(1.65E-04) ,    POU2F1(1.80E-04) ,    POU2F1(1.90E-04)
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
12 (Evi-1__FOXJ2)     28 (Nkx2-5__POU3F2)     38 (Nkx6-2__POU6F1_(c2))     79 (Nkx6-2__POU3F2)     82 (IRF-7A__POU2F1)     145 (COMP1__POU3F2)     175 (HMG_I__POU3F2)     188 (AIRE__Evi-1)     192 (COMP1__Evi-1)     236 (POU6F1_(c2)__Pbx1a)     252 (POU3F2__POU3F2)     274 (IPF1__POU2F1)     323 (AIRE__POU2F1)     361 (HOXA5__POU3F2)     415 (HMG_I__POU6F1_(c2))     421 (Crx__Evi-1)     433 (Nkx6-2__POU2F1)     434 (COMP1__POU2F1)     438 (HOXA5__POU2F1)     463 (Evi-1__Lhx3a)     468 (HNF-6__POU6F1_(c2))     485 (Evi-1__HMG_I)     488 (HNF-6__POU3F2)     492 (Evi-1__POU3F2)     567 (HMG_I__POU2F1)     569 (POU2F1__Pbx1a)     636 (IPF1__POU3F2)     689 (POU6F1_(c2)__PPAR-alpha)     709 (IPF1__POU6F1_(c2))     759 (HNF-6__POU2F1)     766 (POU3F2__Pbx1a)     877 (Evi-1__Pbx1a)     884 (Lhx3a__POU6F1_(c2))     922 (FOXJ2__POU2F1)     929 (Evi-1__IRF-7A)     930 (Lmo2__POU2F1)     966 (AIRE__POU6F1_(c2))     998 (POU2F1__POU3F2)     1016 (FOXJ2__POU6F1_(c2))     1020 (Crx__POU2F1)     1053 (Evi-1__IRF-1)     1127 (IRF-1__POU2F1)     1185 (AIRE__POU3F2)     1186 (POU3F2__PPAR-alpha)     1201 (IRF-7A__POU3F2)     1210 (Crx__POU6F1_(c2))     1221 (Evi-1__IPF1)     1230 (COMP1__POU6F1_(c2))     1233 (FOXJ2__POU3F2)     1234 (Crx__POU3F2)     1307 (Evi-1__Nkx6-2)     1325 (Evi-1__PPAR-alpha)     1336 (POU3F2__POU6F1_(c2))     1357 (Evi-1__HNF-6)     1439 (Evi-1__HOXA5)     1441 (HOXA5__POU6F1_(c2))     1445 (Lhx3a__POU2F1)     1474 (IRF-7A__POU6F1_(c2))     1578 (IRF-1__POU3F2)     1582 (Nkx2-5__POU2F1)     1589 (Lhx3a__POU3F2)     1597 (POU2F1__PPAR-alpha)     1599 (IRF-1__POU6F1_(c2))    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence AATAATTATAsA TwTATAATTATT
Position frequency matrix
1 2 3 4 5 6 7 8 9 10 11 12
A 10 14 3 10 14 0 2 14 3 13 9 12
C 0 0 0 0 0 0 3 0 0 0 0 0
G 0 0 0 0 0 0 0 0 0 0 0 0
T 4 0 11 4 0 14 9 0 11 1 5 2
A A T A A T T A T A n A
1 2 3 4 5 6 7 8 9 10 11 12
A 2 5 1 11 0 9 14 0 4 11 0 4
C 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 3 0 0 0 0 0 0
T 12 9 13 3 14 2 0 14 10 3 14 10
T n T A T A A T T 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
ENSMUSG00000047216 Target Mus musculus chr1:110,854,714-110,854,725 + TATTATCATATA – TATATGATAATA
ENSMUSG00000047216_CFAM Orthologue Canis familiaris chr1:14,098,571-14,098,582 – TATAATTATAAT + ATTATAATTATA
ENSMUSG00000047216_CJAC Orthologue Callithrix jacchus ENSMUSG00000047216_CJAC:422-433 – AATAATTATAAA + TTTATAATTATT
ENSMUSG00000047216_ETEL Orthologue Echinops telfairi scaffold_310853:86,560-86,571 – AATAATTATAAA + TTTATAATTATT
ENSMUSG00000047216_GGAL Orthologue Gallus gallus chr2:95,067,038-95,067,049 – TATTATTATATT + AATATAATAATA
ENSMUSG00000047216_HSAP Orthologue Homo sapiens chr18:62,390,711-62,390,722 + AATAATTATAAA – TTTATAATTATT
ENSMUSG00000047216_MDOM Orthologue Monodelphis domestica scaffold_21:12,262,406-12,262,417 – AAAAATAAAATA + TATTTTATTTTT
ENSMUSG00000047216_MMUL Orthologue Macaca mulatta SCAFFOLD50014:23,033-23,044 + AATAATTATAAA – TTTATAATTATT
ENSMUSG00000047216_OCUN Orthologue Oryctolagus cuniculus scaffold_192255:23,688-23,699 – TAATATCATATA + TATATGATATTA
ENSMUSG00000047216_PPYG Orthologue Pongo pygmaeus ENSMUSG00000047216_PPYG:199-210 – AATAATTATAAA + TTTATAATTATT
ENSMUSG00000047216_PTRO Orthologue Pan troglodytes chr17:59,257,777-59,257,788 + AATAATTATAAA – TTTATAATTATT
ENSMUSG00000047216_RNOR Orthologue Rattus norvegicus chr13:18,233,650-18,233,661 + AATAATTAAATA – TATTTAATTATT
ENSMUSG00000047216_TNIG Orthologue Tetraodon nigroviridis chr11:2,414,342-2,414,353 + AAATATCAAAAA – TTTTTGATATTT
ENSMUSG00000047216_XTRO Orthologue Xenopus tropicalis scaffold_78:1,807,407-1,807,418 – AATAATAATTAA + TTAATTATTATT

Questions or comments: cisred@bcgsc.ca