FILTERS:
pvalue:0.1
Motif craMmus6061
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 craMmus6061
Discovery p-value 2.79E-03
Motif location chr2: 74,503,233-74,503,252 (-) (20 bp)
Search region location chr2: 74,503,074-74,504,854 (-) (1,781 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 25 species: Mus musculus, Bos taurus, Canis familiaris, Callithrix jacchus, Cavia porcellus, Equus caballus, Echinops telfairi, Felis catus, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Myotis lucifugus, Macaca mulatta, Ornithorhynchus anatinus, Otolemur garnettii, Procavia capensis, 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 5 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (5 annot.): IPF1(3.09E-05) ,    HOXA5(2.47E-04) ,    POU6F1_(c2)(2.85E-04) ,    RSRFC4(7.78E-04) ,    HNF-3alpha(8.46E-04)
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
31 (CUTL1__POU6F1_(c2))     38 (Nkx6-2__POU6F1_(c2))     46 (HNF-3__POU6F1_(c2))     77 (FOXP3__HOXA5)     150 (FOXP3__IPF1)     161 (Brachyury__HOXA5)     180 (CUTL1__HOXA5)     274 (IPF1__POU2F1)     351 (AR__HOXA5)     387 (CUTL1__IPF1)     417 (POU6F1_(c2)__POU6F1_(c2))     435 (HOXA5__MEF-2A)     438 (HOXA5__POU2F1)     514 (AIRE__HOXA5)     519 (Evi-1__POU6F1_(c2))     667 (FOXP3__POU6F1_(c2))     709 (IPF1__POU6F1_(c2))     845 (IPF1__MEF-2A)     875 (HOXA5__Nkx6-2)     906 (CREB__IPF1)     942 (POU2F1__POU6F1_(c2))     953 (IPF1__Nkx6-2)     966 (AIRE__POU6F1_(c2))     1221 (Evi-1__IPF1)     1238 (HNF-3__HOXA5)     1271 (MEF-2A__POU6F1_(c2))     1400 (HNF-3alpha__IPF1)     1426 (HNF-3__IPF1)     1439 (Evi-1__HOXA5)     1441 (HOXA5__POU6F1_(c2))     1495 (Brachyury__POU6F1_(c2))     1506 (AIRE__IPF1)     1570 (CREB__HOXA5)     1593 (Brachyury__IPF1)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence TAAATATTATTATCTCTTTT AAAAGAGATAATAATATTTA
Position frequency matrix
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
A 1 20 18 25 0 21 1 0 20 1 1 25 0 5 5 5 1 0 1 0
C 0 0 0 0 0 0 0 0 5 0 0 0 0 20 0 20 4 4 0 5
G 0 0 1 0 0 0 0 5 0 0 0 0 0 0 1 0 0 0 0 4
T 24 5 6 0 25 4 24 20 0 24 24 0 25 0 19 0 20 21 24 16
T A A A T A T T A T T A T C T C T T T T
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
A 16 24 21 20 0 19 0 25 0 24 24 0 20 24 4 25 0 6 5 24
C 4 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 1 0 0
G 5 0 4 4 20 0 20 0 0 0 0 5 0 0 0 0 0 0 0 0
T 0 1 0 1 5 5 5 0 25 1 1 20 0 1 21 0 25 18 20 1
A A A A G A G A T A A T A A T A T T 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
ENSMUSG00000001815 Target Mus musculus chr2:74,503,233-74,503,252 + TAAATATTATTATCTCTTTT – AAAAGAGATAATAATATTTA
ENSMUSG00000001815_BTAU Orthologue Bos taurus chr2:17,082,817-17,082,836 – TAAATATTATTATCTCTTTT + AAAAGAGATAATAATATTTA
ENSMUSG00000001815_CFAM Orthologue Canis familiaris chr36:22,918,340-22,918,359 + TAAATATTATTATCTCTTTT – AAAAGAGATAATAATATTTA
ENSMUSG00000001815_CJAC Orthologue Callithrix jacchus ENSMUSG00000001815_CJAC:1,627-1,646 – TAAATATTATTATCTCTTTC + GAAAGAGATAATAATATTTA
ENSMUSG00000001815_CPOR Orthologue Cavia porcellus ENSMUSG00000001815_CPOR:1,620-1,639 – AATATATTATTATCTCTTTT + AAAAGAGATAATAATATATT
ENSMUSG00000001815_ECAB Orthologue Equus caballus ENSMUSG00000001815_ECAB:1,615-1,634 – TAAATATTATTATCTCTTTT + AAAAGAGATAATAATATTTA
ENSMUSG00000001815_ETEL Orthologue Echinops telfairi scaffold_302036:2,614-2,633 + TAAATATTATTATCTCTTTT – AAAAGAGATAATAATATTTA
ENSMUSG00000001815_FCAT Orthologue Felis catus ENSMUSG00000001815_FCAT:1,635-1,654 – TAAATATTATTATCTCTTTT + AAAAGAGATAATAATATTTA
ENSMUSG00000001815_FRUB Orthologue Fugu rubripes chrUn:297,014,076-297,014,095 + TTTATTTGCTTATAAACCTG – CAGGTTTATAAGCAAATAAA
ENSMUSG00000001815_GGAL Orthologue Gallus gallus chr7:17,118,532-17,118,551 – TAAATATTATTATCTCTTTT + AAAAGAGATAATAATATTTA
ENSMUSG00000001815_HSAP Orthologue Homo sapiens chr2:176,774,109-176,774,128 + TAAATATTATTATCGCTTTC – GAAAGCGATAATAATATTTA
ENSMUSG00000001815_LAFR Orthologue Loxodonta africana scaffold_9144:29,447-29,466 + TTTATTTGCTTATAAACCTG – CAGGTTTATAAGCAAATAAA
ENSMUSG00000001815_MDOM Orthologue Monodelphis domestica scaffold_2:76,041,166-76,041,185 + TAAATATTATTATCTCTTTT – AAAAGAGATAATAATATTTA
ENSMUSG00000001815_MLUC Orthologue Myotis lucifugus ENSMUSG00000001815_MLUC:1,654-1,673 – TAGATATTATTATCTCTTTT + AAAAGAGATAATAATATCTA
ENSMUSG00000001815_MMUL Orthologue Macaca mulatta SCAFFOLD20060:155,608-155,627 + TAAATATTATTATCTCTTTC – GAAAGAGATAATAATATTTA
ENSMUSG00000001815_OANA Orthologue Ornithorhynchus anatinus ENSMUSG00000001815_OANA:200-219 – TTTATAAGCAAATAAACTAC + GTAGTTTATTTGCTTATAAA
ENSMUSG00000001815_OGAR Orthologue Otolemur garnettii ENSMUSG00000001815_OGAR:1,668-1,687 – TAAATATTATTATCTCTTTC + GAAAGAGATAATAATATTTA
ENSMUSG00000001815_PCAP Orthologue Procavia capensis ENSMUSG00000001815_PCAP:550-569 – TAAATATTATTATCTCTTTT + AAAAGAGATAATAATATTTA
ENSMUSG00000001815_PTRO Orthologue Pan troglodytes chr13:66,426,812-66,426,831 – TTTATTTGCTTATAAACCTG + CAGGTTTATAAGCAAATAAA
ENSMUSG00000001815_RNOR Orthologue Rattus norvegicus chr3:57,171,386-57,171,405 + TAAATATTATTATCTCTTTT – AAAAGAGATAATAATATTTA
ENSMUSG00000001815_SARA Orthologue Sorex araneus ENSMUSG00000001815_SARA:1,631-1,650 – TAAATATTATTATCTCTTTT + AAAAGAGATAATAATATTTA
ENSMUSG00000001815_SSCR Orthologue Sus scrofa ENSMUSG00000001815_SSCR:1,607-1,626 – TAAATATTATTATCTCTTTT + AAAAGAGATAATAATATTTA
ENSMUSG00000001815_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000001815_STRI:1,604-1,623 – TAAATATTATTATCTCTTTT + AAAAGAGATAATAATATTTA
ENSMUSG00000001815_TBEL Orthologue Tupaia belangeri ENSMUSG00000001815_TBEL:1,625-1,644 – TAAATATTATTATCTCTTTT + AAAAGAGATAATAATATTTA
ENSMUSG00000001815_XTRO Orthologue Xenopus tropicalis scaffold_353:578,629-578,648 – TTTATTTGCTTATAAAACTG + CAGTTTTATAAGCAAATAAA

Questions or comments: cisred@bcgsc.ca