FILTERS:
pvalue:0.1
Motif craMmus404983
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 craMmus404983
Discovery p-value 2.79E-03
Motif location chr2: 87,450,393-87,450,402 (+) (10 bp)
Search region location chr2: 87,449,551-87,451,305 (+) (1,755 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 16 species: Mus musculus, Bos taurus, Canis familiaris, Dasypus novemcinctus, Danio rerio, Echinops telfairi, Fugu rubripes, Gallus gallus, Loxodonta africana, Monodelphis domestica, Macropus eugenii, Rattus norvegicus, Sorex araneus, 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: (7 annot.): aMEF-2(7.62E-05) ,    Crx(9.22E-05) ,    MEF-2A(3.27E-04) ,    FOXJ2(3.51E-04) ,    HMG_I(5.09E-04) ...
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
12 (Evi-1__FOXJ2)     18 (FOXD3__aMEF-2)     22 (Brachyury__aMEF-2)     24 (Brachyury__MEF-2A)     43 (MEF-2A__POU3F2)     68 (CREB__aMEF-2)     70 (FOXJ2__SRY)     138 (FOXJ2__RSRFC4)     154 (FOXJ2__MRF-2)     182 (MEF-2A__MRF-2)     245 (FOXJ2__FOXP1a)     317 (POU6F1_(c2)__aMEF-2)     355 (FOXP1a__aMEF-2)     399 (POU3F2__aMEF-2)     421 (Crx__Evi-1)     566 (FOXJ2__Nkx6-2)     577 (MEF-2A__OCA-B)     613 (FOXD3__FOXJ2)     643 (Crx__RSRFC4)     669 (Evi-1__MEF-2A)     785 (Hlf__MEF-2A)     802 (POU3F1__aMEF-2)     817 (Nkx6-2__aMEF-2)     851 (POU2F1__aMEF-2)     869 (Evi-1__aMEF-2)     871 (MEF-2A__POU2F1)     917 (FOXJ2__POU3F1)     922 (FOXJ2__POU2F1)     934 (RSRFC4__aMEF-2)     936 (MEF-2A__RSRFC4)     939 (MEF-2A__Nkx6-2)     1016 (FOXJ2__POU6F1_(c2))     1019 (CAR__MEF-2A)     1020 (Crx__POU2F1)     1055 (SRY__aMEF-2)     1086 (Crx__FOXP1a)     1108 (C-EBPbeta__FOXJ2)     1210 (Crx__POU6F1_(c2))     1233 (FOXJ2__POU3F2)     1234 (Crx__POU3F2)     1235 (MEF-2A__POU3F1)     1259 (FOXP1a__MEF-2A)     1265 (C-EBPbeta__aMEF-2)     1271 (MEF-2A__POU6F1_(c2))     1324 (C-EBPbeta__MEF-2A)     1326 (HP1_site_factor__MEF-2A)     1378 (FOXD3__MEF-2A)     1391 (OCA-B__aMEF-2)     1404 (Hlf__aMEF-2)     1415 (Crx__Nkx6-2)     1431 (FOXJ2__Hlf)     1433 (FOXJ2__OCA-B)     1461 (HP1_site_factor__aMEF-2)     1462 (MEF-2A__SRY)     1473 (MRF-2__aMEF-2)     1540 (CAR__aMEF-2)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence TTGTTATTAT ATAATAACAA
Position frequency matrix
1 2 3 4 5 6 7 8 9 10
A 3 3 4 1 4 16 0 5 16 0
C 3 0 0 0 1 0 0 0 0 1
G 0 0 12 0 0 0 0 1 0 0
T 10 13 0 15 11 0 16 10 0 15
T T G T T A T T A T
1 2 3 4 5 6 7 8 9 10
A 15 0 10 16 0 11 15 0 13 10
C 0 0 1 0 0 0 0 12 0 0
G 1 0 0 0 0 1 0 0 0 3
T 0 16 5 0 16 4 1 4 3 3
A T A A T A A C 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
ENSMUSG00000059205 Target Mus musculus chr2:87,450,393-87,450,402 + AAGTTATTAT – ATAATAACTT
ENSMUSG00000059205_BTAU Orthologue Bos taurus chr2:606,210-606,219 + ATATTATTAT – ATAATAATAT
ENSMUSG00000059205_CFAM Orthologue Canis familiaris chr18:43,005,078-43,005,087 + ATGTTATTAT – ATAATAACAT
ENSMUSG00000059205_DNOV Orthologue Dasypus novemcinctus scaffold_90506:5,602-5,611 – TTGTAATTAT + ATAATTACAA
ENSMUSG00000059205_DRER Orthologue Danio rerio chr21:38,705,727-38,705,736 + TTGTAATAAT – ATTATTACAA
ENSMUSG00000059205_ETEL Orthologue Echinops telfairi scaffold_240389:11,316-11,325 + TTGATATTAT – ATAATATCAA
ENSMUSG00000059205_FRUB Orthologue Fugu rubripes chrUn:320,826,605-320,826,614 – CTGTTATTAT + ATAATAACAG
ENSMUSG00000059205_GGAL Orthologue Gallus gallus chr5:2,410,195-2,410,204 + CTGTTATTAT – ATAATAACAG
ENSMUSG00000059205_LAFR Orthologue Loxodonta africana scaffold_144:35,798-35,807 – TTGTTATAAT + ATTATAACAA
ENSMUSG00000059205_MDOM Orthologue Monodelphis domestica scaffold_33:17,289,862-17,289,871 – TAGTTATAAT + ATTATAACTA
ENSMUSG00000059205_MEUG Orthologue Macropus eugenii ENSMUSG00000059205_MEUG:477-486 + CTATAATAAT – ATTATTATAG
ENSMUSG00000059205_RNOR Orthologue Rattus norvegicus chr3:70,246,816-70,246,825 – TTGTTATGAT + ATCATAACAA
ENSMUSG00000059205_SARA Orthologue Sorex araneus ENSMUSG00000059205_SARA:552-561 – TTATTATTAT + ATAATAATAA
ENSMUSG00000059205_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000059205_STRI:351-360 + TAGTCATAAT – ATTATGACTA
ENSMUSG00000059205_TBEL Orthologue Tupaia belangeri ENSMUSG00000059205_TBEL:234-243 – TTGTTATTAC + GTAATAACAA
ENSMUSG00000059205_XTRO Orthologue Xenopus tropicalis scaffold_10:3,876,804-3,876,813 + TTATAATTAT – ATAATTATAA

Questions or comments: cisred@bcgsc.ca