FILTERS:
pvalue:0.1
Motif craMmus292425
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 craMmus292425
Discovery p-value 2.79E-03
Motif location chr17: 36,379,122-36,379,129 (+) (8 bp)
Search region location chr17: 36,378,119-36,380,280 (+) (2,162 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 15 species: Mus musculus, Bos taurus, Choloepus hoffmanni, Dasypus novemcinctus, Danio rerio, Erinaceus europaeus, Echinops telfairi, Gallus gallus, Homo sapiens, Macaca mulatta, Oryctolagus cuniculus, Pan troglodytes, Rattus norvegicus, 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 8 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (8 annot.): CUTL1(9.84E-05) ,    Chx10(2.02E-04) ,    POU6F1_(c2)(2.85E-04) ,    AFP1(3.32E-04) ,    aMEF-2(6.87E-04) ...
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
27 (CUTL1__YY1)     31 (CUTL1__POU6F1_(c2))     44 (CUTL1__Evi-1)     46 (HNF-3__POU6F1_(c2))     118 (Chx10__Evi-1)     180 (CUTL1__HOXA5)     222 (POU6F1_(c2)__YY1)     250 (POU6F1_(c2)__RSRFC4)     254 (Cdx-2__Chx10)     271 (CUTL1__RSRFC4)     329 (CUTL1__Chx10)     417 (POU6F1_(c2)__POU6F1_(c2))     437 (CUTL1__Cdx-2)     498 (Chx10__HOXA5)     519 (Evi-1__POU6F1_(c2))     525 (AFP1__Chx10)     526 (CUTL1__CUTL1)     545 (CUTL1__HNF-3)     611 (Chx10__POU1F1)     627 (AFP1__RSRFC4)     639 (Chx10__Crx)     700 (AFP1__HOXA5)     715 (CUTL1__Crx)     826 (Chx10__YY1)     880 (CUTL1__POU1F1)     881 (AFP1__CUTL1)     914 (Chx10__POU6F1_(c2))     955 (AFP1__YY1)     1069 (POU1F1__POU6F1_(c2))     1175 (AFP1__Evi-1)     1204 (AFP1__HNF-3)     1210 (Crx__POU6F1_(c2))     1394 (Chx10__Chx10)     1410 (Cdx-2__POU6F1_(c2))     1424 (Chx10__SRF)     1429 (Chx10__RSRFC4)     1441 (HOXA5__POU6F1_(c2))     1455 (CUTL1__SRF)     1503 (Chx10__HNF-3)     1517 (AFP1__POU1F1)     1534 (AFP1__POU6F1_(c2))     1547 (AFP1__Cdx-2)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence TyTAATTT AAATTArA
Position frequency matrix
1 2 3 4 5 6 7 8
A 0 3 0 15 15 0 0 0
C 0 5 3 0 0 3 0 0
G 0 0 0 0 0 0 0 0
T 15 7 12 0 0 12 15 15
T y T A A T T T
1 2 3 4 5 6 7 8
A 15 15 12 0 0 12 7 15
C 0 0 0 0 0 0 0 0
G 0 0 3 0 0 3 5 0
T 0 0 0 15 15 0 3 0
A A A T T A r 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
ENSMUSG00000057801 Target Mus musculus chr17:36,379,122-36,379,129 + TATAATTT – AAATTATA
ENSMUSG00000057801_BTAU Orthologue Bos taurus chr3:62,411,330-62,411,337 – TTTAATTT + AAATTAAA
ENSMUSG00000057801_CHOF Orthologue Choloepus hoffmanni ENSMUSG00000057801_CHOF:343-350 – TCTAACTT + AAGTTAGA
ENSMUSG00000057801_DNOV Orthologue Dasypus novemcinctus scaffold_71203:638-645 – TCTAATTT + AAATTAGA
ENSMUSG00000057801_DRER Orthologue Danio rerio chr15:36,004,560-36,004,567 – TTTAATTT + AAATTAAA
ENSMUSG00000057801_EEUR Orthologue Erinaceus europaeus ENSMUSG00000057801_EEUR:114-121 – TCCAATTT + AAATTGGA
ENSMUSG00000057801_ETEL Orthologue Echinops telfairi scaffold_35478:2,178-2,185 – TCTAACTT + AAGTTAGA
ENSMUSG00000057801_GGAL Orthologue Gallus gallus chr5:2,409,137-2,409,144 + TATAATTT – AAATTATA
ENSMUSG00000057801_HSAP Orthologue Homo sapiens chr6:29,214,577-29,214,584 + TTCAATTT – AAATTGAA
ENSMUSG00000057801_MMUL Orthologue Macaca mulatta SCAFFOLD35633:13,174-13,181 + TTTAATTT – AAATTAAA
ENSMUSG00000057801_OCUN Orthologue Oryctolagus cuniculus scaffold_185279:5,354-5,361 – TCTAACTT + AAGTTAGA
ENSMUSG00000057801_PTRO Orthologue Pan troglodytes chr5:29,737,145-29,737,152 + TTCAATTT – AAATTGAA
ENSMUSG00000057801_RNOR Orthologue Rattus norvegicus chr20:189,115-189,122 + TATAATTT – AAATTATA
ENSMUSG00000057801_TBEL Orthologue Tupaia belangeri ENSMUSG00000057801_TBEL:151-158 – TTTAATTT + AAATTAAA
ENSMUSG00000057801_XTRO Orthologue Xenopus tropicalis scaffold_786:552,423-552,430 – TTTAATTT + AAATTAAA

Questions or comments: cisred@bcgsc.ca