FILTERS:
pvalue:0.1
Motif craMmus420642
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 craMmus420642
Discovery p-value 2.79E-03
Motif location chr7: 104,262,841-104,262,850 (-) (10 bp)
Search region location chr7: 104,261,736-104,263,456 (-) (1,721 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 20 species: Mus musculus, Canis familiaris, Callithrix jacchus, Cavia porcellus, Dasypus novemcinctus, Equus caballus, Erinaceus europaeus, Echinops telfairi, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Procavia capensis, Pan troglodytes, Rattus norvegicus, Sorex araneus, Tupaia belangeri
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: (10 annot.): RSRFC4(1.04E-04) ,    RSRFC4(1.18E-04) ,    Nkx6-2(2.01E-04) ,    TEF(2.38E-04) ,    aMEF-2(4.71E-04) ...
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
34 (Nkx6-2__Nkx6-2)     38 (Nkx6-2__POU6F1_(c2))     79 (Nkx6-2__POU3F2)     97 (HNF-1alpha__TEF)     127 (HFH-1__Nkx6-2)     166 (FOXD3__Nkx6-2)     219 (HNF-1alpha__RSRFC4)     250 (POU6F1_(c2)__RSRFC4)     273 (HFH-1__RSRFC4)     334 (HFH-1__TEF)     348 (Nkx6-2__TEF)     433 (Nkx6-2__POU2F1)     503 (Nkx6-2__RSRFC4)     548 (POU6F1_(c2)__TEF)     578 (E4BP4__Nkx6-2)     602 (HNF-1alpha__Nkx6-2)     650 (E4BP4__TEF)     651 (Pax-8__RSRFC4)     727 (FOXD3__TEF)     777 (RSRFC4__TEF)     798 (E4BP4__RSRFC4)     800 (POU2F1__TEF)     817 (Nkx6-2__aMEF-2)     903 (TEF__aMEF-2)     934 (RSRFC4__aMEF-2)     936 (MEF-2A__RSRFC4)     939 (MEF-2A__Nkx6-2)     944 (POU3F2__RSRFC4)     989 (POU2F1__RSRFC4)     994 (Chx10__TEF)     1041 (RSRFC4__RSRFC4)     1104 (Nkx6-2__POU1F1)     1167 (POU3F2__TEF)     1196 (POU1F1__TEF)     1290 (MEF-2A__TEF)     1293 (FOXD3__RSRFC4)     1363 (POU1F1__RSRFC4)     1429 (Chx10__RSRFC4)     1559 (Chx10__Nkx6-2)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence ATATTTnsAT ATwnAAATAT
Position frequency matrix
1 2 3 4 5 6 7 8 9 10
A 20 0 18 5 1 2 8 12 20 0
C 0 0 0 0 0 2 5 0 0 0
G 0 0 2 0 5 0 0 0 0 0
T 0 20 0 15 14 16 7 8 0 20
A T A T T T n w A T
1 2 3 4 5 6 7 8 9 10
A 20 0 8 7 16 14 15 0 20 0
C 0 0 0 0 0 5 0 2 0 0
G 0 0 0 5 2 0 0 0 0 0
T 0 20 12 8 2 1 5 18 0 20
A T w n A A A T 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
ENSMUSG00000062710 Target Mus musculus chr7:104,262,841-104,262,850 + ATATTTAAAT – ATTTAAATAT
ENSMUSG00000062710_CFAM Orthologue Canis familiaris chr21:34,596,200-34,596,209 + ATATGTCAAT – ATTGACATAT
ENSMUSG00000062710_CJAC Orthologue Callithrix jacchus ENSMUSG00000062710_CJAC:1,501-1,510 + ATATTTTAAT – ATTAAAATAT
ENSMUSG00000062710_CPOR Orthologue Cavia porcellus ENSMUSG00000062710_CPOR:53-62 – ATAATTCTAT + ATAGAATTAT
ENSMUSG00000062710_DNOV Orthologue Dasypus novemcinctus scaffold_61181:1,434-1,443 – ATAAGCATAT + ATATGCTTAT
ENSMUSG00000062710_ECAB Orthologue Equus caballus ENSMUSG00000062710_ECAB:410-419 – ATATGTTTAT + ATAAACATAT
ENSMUSG00000062710_EEUR Orthologue Erinaceus europaeus ENSMUSG00000062710_EEUR:136-145 + ATAAGACAAT – ATTGTCTTAT
ENSMUSG00000062710_ETEL Orthologue Echinops telfairi scaffold_293626:79,905-79,914 + ATATTTATAT – ATATAAATAT
ENSMUSG00000062710_FRUB Orthologue Fugu rubripes chrUn:265,454,776-265,454,785 + ATATTCTAAT – ATTAGAATAT
ENSMUSG00000062710_GGAL Orthologue Gallus gallus chr5:57,671-57,680 – ATGATTCTAT + ATAGAATCAT
ENSMUSG00000062710_HSAP Orthologue Homo sapiens chr11:7,776,093-7,776,102 – ATATTTTAAT + ATTAAAATAT
ENSMUSG00000062710_LAFR Orthologue Loxodonta africana scaffold_12075:7,212-7,221 – ATGTTTTTAT + ATAAAAACAT
ENSMUSG00000062710_MDOM Orthologue Monodelphis domestica scaffold_33:18,374,027-18,374,036 – ATATATAAAT + ATTTATATAT
ENSMUSG00000062710_MMUL Orthologue Macaca mulatta SCAFFOLD105816:45,666-45,675 + ATATTTTAAT – ATTAAAATAT
ENSMUSG00000062710_OCUN Orthologue Oryctolagus cuniculus scaffold_207842:13,149-13,158 – ATATGAAAAT + ATTTTCATAT
ENSMUSG00000062710_PCAP Orthologue Procavia capensis ENSMUSG00000062710_PCAP:475-484 + ATAATTCAAT – ATTGAATTAT
ENSMUSG00000062710_PTRO Orthologue Pan troglodytes chr9:7,896,191-7,896,200 – ATATTTTAAT + ATTAAAATAT
ENSMUSG00000062710_RNOR Orthologue Rattus norvegicus chr1:165,932,640-165,932,649 + ATATTTAAAT – ATTTAAATAT
ENSMUSG00000062710_SARA Orthologue Sorex araneus ENSMUSG00000062710_SARA:470-479 – ATATTTATAT + ATATAAATAT
ENSMUSG00000062710_TBEL Orthologue Tupaia belangeri ENSMUSG00000062710_TBEL:200-209 – ATATTTATAT + ATATAAATAT

Questions or comments: cisred@bcgsc.ca