FILTERS:
pvalue:0.1
Motif craMmus294929
More information about this gene at Ensembl.org Go to UCSC
The contents of this page can be modified by changing your filter settings.
Currently, this page only shows information about a motif if it:
+ has a discovery p-value < 0.1
Filters based on species and motif discovery algorithms are not applied to the contents of this page.

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 craMmus294929
Discovery p-value 2.79E-03
Motif location chr7: 104,439,008-104,439,015 (-) (8 bp)
Search region location chr7: 104,438,705-104,440,680 (-) (1,976 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 23 species: Mus musculus, Canis familiaris, Choloepus hoffmanni, Dasypus novemcinctus, Danio rerio, Erinaceus europaeus, Echinops telfairi, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Myotis lucifugus, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, 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 9 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (8 annot.): RSRFC4(1.14E-04) ,    RSRFC4(1.54E-04) ,    Nkx6-2(2.01E-04) ,    TEF(2.38E-04) ,    POU2F1(4.12E-04) ...
ORegAnno: (1 annot.): FoxA1(6.44E-04)
Modules
(Co-occurring motif patterns)		 Annotation-based:
42 (HP1_site_factor__Nkx6-2)     84 (Nkx3-1__TEF)     110 (Nkx6-2__OCA-B)     119 (Nkx6-2__YY1)     173 (FOXP1a__TEF)     243 (FOXP1a__Nkx6-2)     249 (HMG_I__RSRFC4)     271 (CUTL1__RSRFC4)     320 (CUTL1__TEF)     433 (Nkx6-2__POU2F1)     446 (Evi-1__RSRFC4)     454 (CREB__Nkx6-2)     457 (IRF-1__Nkx6-2)     474 (HNF-6__TEF)     493 (AIRE__Nkx6-2)     503 (Nkx6-2__RSRFC4)     561 (HMG_I__TEF)     605 (HP1_site_factor__RSRFC4)     676 (FOXP1a__RSRFC4)     775 (RSRFC4__YY1)     777 (RSRFC4__TEF)     800 (POU2F1__TEF)     820 (Evi-1__TEF)     883 (TEF__YY1)     895 (HNF-6__Nkx6-2)     936 (MEF-2A__RSRFC4)     939 (MEF-2A__Nkx6-2)     946 (OCA-B__RSRFC4)     989 (POU2F1__RSRFC4)     1013 (Nkx6-2__S8)     1017 (HMG_I__Nkx6-2)     1041 (RSRFC4__RSRFC4)     1047 (HNF-6__RSRFC4)     1146 (Nkx3-1__RSRFC4)     1190 (AIRE__TEF)     1193 (OCA-B__TEF)     1195 (IRF-1__TEF)     1216 (S8__TEF)     1283 (Nkx6-2__POU3F1)     1287 (Nkx3-1__Nkx6-2)     1290 (MEF-2A__TEF)     1307 (Evi-1__Nkx6-2)     1358 (CUTL1__Nkx6-2)     1446 (IRF-1__RSRFC4)     1452 (RSRFC4__S8)     1467 (POU3F1__RSRFC4)     1515 (CREB__RSRFC4)     1529 (AIRE__RSRFC4)     1545 (POU3F1__TEF)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence TATATTTT AAAATATA
Position frequency matrix
1 2 3 4 5 6 7 8
A 0 17 0 23 0 0 7 7
C 0 0 1 0 0 0 0 0
G 0 6 0 0 4 0 0 0
T 23 0 22 0 19 23 16 16
T A T A T T T T
1 2 3 4 5 6 7 8
A 16 16 23 19 0 22 0 23
C 0 0 0 4 0 0 6 0
G 0 0 0 0 0 1 0 0
T 7 7 0 0 23 0 17 0
A A A A T A T 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
ENSMUSG00000058014 Target Mus musculus chr7:104,439,008-104,439,015 + TATATTTA – TAAATATA
ENSMUSG00000058014_CFAM Orthologue Canis familiaris chr21:34,594,847-34,594,854 – TGTATTTT + AAAATACA
ENSMUSG00000058014_CHOF Orthologue Choloepus hoffmanni ENSMUSG00000058014_CHOF:381-388 + TGTATTTA – TAAATACA
ENSMUSG00000058014_DNOV Orthologue Dasypus novemcinctus scaffold_61181:1,761-1,768 + TGTATTAA – TTAATACA
ENSMUSG00000058014_DRER Orthologue Danio rerio chr15:35,900,596-35,900,603 – TATATTAT + ATAATATA
ENSMUSG00000058014_EEUR Orthologue Erinaceus europaeus ENSMUSG00000058014_EEUR:223-230 + TACATTTT – AAAATGTA
ENSMUSG00000058014_ETEL Orthologue Echinops telfairi scaffold_293626:80,765-80,772 – TATATTAT + ATAATATA
ENSMUSG00000058014_FRUB Orthologue Fugu rubripes chrUn:304,385,791-304,385,798 – TATAGTTA + TAACTATA
ENSMUSG00000058014_GGAL Orthologue Gallus gallus chr5:54,445-54,452 – TATAGTAT + ATACTATA
ENSMUSG00000058014_HSAP Orthologue Homo sapiens chr11:7,775,262-7,775,269 + TATATTTT – AAAATATA
ENSMUSG00000058014_LAFR Orthologue Loxodonta africana scaffold_17479:62,218-62,225 – TATATTTT + AAAATATA
ENSMUSG00000058014_MDOM Orthologue Monodelphis domestica scaffold_33:18,809,016-18,809,023 – TATAGTTA + TAACTATA
ENSMUSG00000058014_MLUC Orthologue Myotis lucifugus ENSMUSG00000058014_MLUC:1,908-1,915 + TGTATTTT – AAAATACA
ENSMUSG00000058014_MMUL Orthologue Macaca mulatta SCAFFOLD105816:44,822-44,829 + TATATTAT – ATAATATA
ENSMUSG00000058014_OCUN Orthologue Oryctolagus cuniculus scaffold_207842:14,159-14,166 – TATATTTA + TAAATATA
ENSMUSG00000058014_OGAR Orthologue Otolemur garnettii ENSMUSG00000058014_OGAR:203-210 + TATATTTT – AAAATATA
ENSMUSG00000058014_PTRO Orthologue Pan troglodytes chr9:7,895,377-7,895,384 + TATATTTT – AAAATATA
ENSMUSG00000058014_RNOR Orthologue Rattus norvegicus chr1:165,653,065-165,653,072 + TATATTAT – ATAATATA
ENSMUSG00000058014_SARA Orthologue Sorex araneus ENSMUSG00000058014_SARA:1-8 + TGTATTAT – ATAATACA
ENSMUSG00000058014_SSCR Orthologue Sus scrofa ENSMUSG00000058014_SSCR:474-481 + TGTATTTT – AAAATACA
ENSMUSG00000058014_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000058014_STRI:336-343 + TATATTTT – AAAATATA
ENSMUSG00000058014_TBEL Orthologue Tupaia belangeri ENSMUSG00000058014_TBEL:309-316 + TATATTTT – AAAATATA
ENSMUSG00000058014_XTRO Orthologue Xenopus tropicalis scaffold_10:4,501,806-4,501,813 – TATAGTTA + TAACTATA

Questions or comments: cisred@bcgsc.ca