FILTERS:
pvalue:0.1
Motif craMmus123226
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 craMmus123226
Discovery p-value 2.79E-03
Motif location chr2: 168,559,815-168,559,820 (-) (6 bp)
Search region location chr2: 168,559,601-168,561,300 (-) (1,700 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 23 species: Mus musculus, Bos taurus, Callithrix jacchus, Danio rerio, Equus caballus, Erinaceus europaeus, Echinops telfairi, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Myotis lucifugus, Macaca mulatta, Ornithorhynchus anatinus, Otolemur garnettii, Procavia capensis, Pan troglodytes, Sorex araneus, Spermophilus tridecemlineatus, Tupaia belangeri, Tetraodon nigroviridis, 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.): Pax-8(2.86E-05) ,    HOXA5(4.29E-05) ,    Pax-8(2.92E-04) ,    Pax-2(6.45E-04) ,    HNF-1alpha(8.28E-04)
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence TGCATT AATGCA
Position frequency matrix
1 2 3 4 5 6
A 0 0 0 23 0 0
C 0 0 23 0 0 0
G 0 23 0 0 0 0
T 23 0 0 0 23 23
T G C A T T
1 2 3 4 5 6
A 23 23 0 0 0 23
C 0 0 0 0 23 0
G 0 0 0 23 0 0
T 0 0 23 0 0 0
A A T G C 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
ENSMUSG00000027547 Target Mus musculus chr2:168,559,815-168,559,820 + TGCATT – AATGCA
ENSMUSG00000027547_BTAU Orthologue Bos taurus chr13:58,354,468-58,354,473 – TGCATT + AATGCA
ENSMUSG00000027547_CJAC Orthologue Callithrix jacchus ENSMUSG00000027547_CJAC:23-28 + TGCATT – AATGCA
ENSMUSG00000027547_DRER Orthologue Danio rerio chr6:10,463,371-10,463,376 + TGCATT – AATGCA
ENSMUSG00000027547_ECAB Orthologue Equus caballus ENSMUSG00000027547_ECAB:465-470 + TGCATT – AATGCA
ENSMUSG00000027547_EEUR Orthologue Erinaceus europaeus ENSMUSG00000027547_EEUR:269-274 + TGCATT – AATGCA
ENSMUSG00000027547_ETEL Orthologue Echinops telfairi scaffold_277629:51,994-51,999 + TGCATT – AATGCA
ENSMUSG00000027547_FRUB Orthologue Fugu rubripes chrUn:40,043,392-40,043,397 + TGCATT – AATGCA
ENSMUSG00000027547_GGAL Orthologue Gallus gallus chr11:5,950,735-5,950,740 + TGCATT – AATGCA
ENSMUSG00000027547_HSAP Orthologue Homo sapiens chr20:49,852,480-49,852,485 – TGCATT + AATGCA
ENSMUSG00000027547_LAFR Orthologue Loxodonta africana scaffold_23735:32,382-32,387 – TGCATT + AATGCA
ENSMUSG00000027547_MDOM Orthologue Monodelphis domestica scaffold_1:164,016,141-164,016,146 – TGCATT + AATGCA
ENSMUSG00000027547_MLUC Orthologue Myotis lucifugus ENSMUSG00000027547_MLUC:279-284 + TGCATT – AATGCA
ENSMUSG00000027547_MMUL Orthologue Macaca mulatta SCAFFOLD106083:10,222-10,227 – TGCATT + AATGCA
ENSMUSG00000027547_OANA Orthologue Ornithorhynchus anatinus ENSMUSG00000027547_OANA:123-128 + TGCATT – AATGCA
ENSMUSG00000027547_OGAR Orthologue Otolemur garnettii ENSMUSG00000027547_OGAR:1,557-1,562 + TGCATT – AATGCA
ENSMUSG00000027547_PCAP Orthologue Procavia capensis ENSMUSG00000027547_PCAP:466-471 + TGCATT – AATGCA
ENSMUSG00000027547_PTRO Orthologue Pan troglodytes chr21:52,618,346-52,618,351 – TGCATT + AATGCA
ENSMUSG00000027547_SARA Orthologue Sorex araneus ENSMUSG00000027547_SARA:184-189 + TGCATT – AATGCA
ENSMUSG00000027547_STRI Orthologue Spermophilus tridecemlineatus ENSMUSG00000027547_STRI:1,423-1,428 + TGCATT – AATGCA
ENSMUSG00000027547_TBEL Orthologue Tupaia belangeri ENSMUSG00000027547_TBEL:531-536 + TGCATT – AATGCA
ENSMUSG00000027547_TNIG Orthologue Tetraodon nigroviridis chr9:9,787,738-9,787,743 – TGCATT + AATGCA
ENSMUSG00000027547_XTRO Orthologue Xenopus tropicalis scaffold_165:1,768,713-1,768,718 – TGCATT + AATGCA

Questions or comments: cisred@bcgsc.ca