FILTERS:
pvalue:0.1
Motif craMmus394126
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 craMmus394126
Discovery p-value 2.79E-03
Motif location chr11: 96,390,915-96,390,926 (+) (12 bp)
Search region location chr11: 96,389,405-96,391,143 (+) (1,739 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 25 species: Mus musculus, Bos taurus, Canis familiaris, Callithrix jacchus, Cavia porcellus, Danio rerio, Equus caballus, Erinaceus europaeus, Echinops telfairi, Gallus gallus, Homo sapiens, Monodelphis domestica, Macropus eugenii, Myotis lucifugus, Macaca mulatta, Oryctolagus cuniculus, Procavia capensis, Pongo pygmaeus, Pan troglodytes, Rattus norvegicus, Sorex araneus, Sus scrofa, Spermophilus tridecemlineatus, Tupaia belangeri, 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: (6 annot.): POU6F1_(c2)(1.47E-04) ,    HNF-1alpha(3.60E-04) ,    POU1F1(6.22E-04) ,    HOXA5(6.90E-04) ,    Pbx1a(7.51E-04) ...
ORegAnno: (1 annot.): FoxA1(2.76E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
23 (HNF-1alpha__Pax-6)     31 (CUTL1__POU6F1_(c2))     38 (Nkx6-2__POU6F1_(c2))     46 (HNF-3__POU6F1_(c2))     60 (Cdx-2__HNF-1alpha)     83 (C-EBPalpha__HNF-1alpha)     111 (CUTL1__HNF-1alpha)     152 (HNF-1alpha__IRF-7A)     185 (HNF-1alpha__HNF-3)     215 (HNF-1alpha__YY1)     218 (HNF-1alpha__HOXA3)     222 (POU6F1_(c2)__YY1)     285 (HNF-1alpha__POU6F1_(c2))     317 (POU6F1_(c2)__aMEF-2)     479 (Cdc5__HNF-1alpha)     602 (HNF-1alpha__Nkx6-2)     644 (HFH-1__HNF-1alpha)     690 (Cdc5__POU6F1_(c2))     709 (IPF1__POU6F1_(c2))     767 (HNF-1alpha__aMEF-2)     772 (POU6F1_(c2)__Pax-6)     774 (HNF-1alpha__POU2F1)     844 (HNF-1alpha__Msx-1)     942 (POU2F1__POU6F1_(c2))     1000 (HNF-1alpha__IPF1)     1021 (HNF-1alpha__Sox9)     1072 (POU6F1_(c2)__Sox9)     1076 (CAR__HNF-1alpha)     1147 (HNF-1alpha__S8)     1177 (POU6F1_(c2)__S8)     1254 (HNF-1alpha__HNF-1alpha)     1410 (Cdx-2__POU6F1_(c2))     1457 (POU3F1__POU6F1_(c2))     1474 (IRF-7A__POU6F1_(c2))     1492 (HNF-1alpha__POU3F1)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence TTTATCAATAAT ATTATTGATAAA
Position frequency matrix
1 2 3 4 5 6 7 8 9 10 11 12
A 0 0 0 25 0 0 25 25 3 25 21 1
C 0 0 0 0 0 21 0 0 0 0 0 2
G 0 4 0 0 0 0 0 0 0 0 0 0
T 25 21 25 0 25 4 0 0 22 0 4 22
T T T A T C A A T A A T
1 2 3 4 5 6 7 8 9 10 11 12
A 22 4 0 22 0 0 4 25 0 25 21 25
C 0 0 0 0 0 0 0 0 0 0 4 0
G 2 0 0 0 0 0 21 0 0 0 0 0
T 1 21 25 3 25 25 0 0 25 0 0 0
A T T A T T G A T A A 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
ENSMUSG00000056648 Target Mus musculus chr11:96,390,915-96,390,926 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_BTAU Orthologue Bos taurus chr19:31,232,390-31,232,401 – TTTATCAATAAT + ATTATTGATAAA
ENSMUSG00000056648_CFAM Orthologue Canis familiaris chr9:28,205,279-28,205,290 – TTTATCAATAAT + ATTATTGATAAA
ENSMUSG00000056648_CJAC Orthologue Callithrix jacchus ENSMUSG00000056648_CJAC:1,565-1,576 + TTTATCAATATT – AATATTGATAAA
ENSMUSG00000056648_CPOR Orthologue Cavia porcellus ENSMUSG00000056648_CPOR:310-321 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_DRER Orthologue Danio rerio chr23:49,496,459-49,496,470 + TGTATTAATAAT – ATTATTAATACA
ENSMUSG00000056648_ECAB Orthologue Equus caballus ENSMUSG00000056648_ECAB:122-133 + TGTATTAAAATA – TATTTTAATACA
ENSMUSG00000056648_EEUR Orthologue Erinaceus europaeus ENSMUSG00000056648_EEUR:87-98 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_ETEL Orthologue Echinops telfairi scaffold_316744:59,823-59,834 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_GGAL Orthologue Gallus gallus chr27:2,226,667-2,226,678 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_HSAP Orthologue Homo sapiens chr17:44,048,133-44,048,144 – TTTATCAATAAT + ATTATTGATAAA
ENSMUSG00000056648_MDOM Orthologue Monodelphis domestica scaffold_18:45,581,275-45,581,286 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_MEUG Orthologue Macropus eugenii ENSMUSG00000056648_MEUG:229-240 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_MLUC Orthologue Myotis lucifugus ENSMUSG00000056648_MLUC:632-643 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_MMUL Orthologue Macaca mulatta SCAFFOLD60055:57,719-57,730 – TTTATCAATAAT + ATTATTGATAAA
ENSMUSG00000056648_OCUN Orthologue Oryctolagus cuniculus scaffold_203826:148,119-148,130 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_PCAP Orthologue Procavia capensis ENSMUSG00000056648_PCAP:476-487 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_PPYG Orthologue Pongo pygmaeus ENSMUSG00000056648_PPYG:636-647 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_PTRO Orthologue Pan troglodytes 19_random:42,997,113-42,997,124 – TTTATCAATAAT + ATTATTGATAAA
ENSMUSG00000056648_RNOR Orthologue Rattus norvegicus chr10:85,027,115-85,027,126 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_SARA Orthologue Sorex araneus ENSMUSG00000056648_SARA:353-364 + TGTATTAAAATC – GATTTTAATACA
ENSMUSG00000056648_SSCR Orthologue Sus scrofa ENSMUSG00000056648_SSCR:373-384 + TGTATTAAAATC – GATTTTAATACA
ENSMUSG00000056648_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000056648_STRI:369-380 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_TBEL Orthologue Tupaia belangeri ENSMUSG00000056648_TBEL:616-627 + TTTATCAATAAT – ATTATTGATAAA
ENSMUSG00000056648_XTRO Orthologue Xenopus tropicalis scaffold_329:584,781-584,792 – TTTATCAATAAT + ATTATTGATAAA

Questions or comments: cisred@bcgsc.ca