FILTERS:
pvalue:0.1
Motif craMmus228321
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 craMmus228321
Discovery p-value 2.79E-03
Motif location chr3: 112,976,115-112,976,126 (-) (12 bp)
Search region location chr3: 112,974,669-112,977,055 (-) (2,387 bp)
Assembly Mouse, Ensembl v38 (NCBI m35)
Found in 21 species: Mus musculus, Canis familiaris, Choloepus hoffmanni, Callithrix jacchus, Dasypus novemcinctus, Equus caballus, Echinops telfairi, Fugu rubripes, Gallus gallus, Homo sapiens, Loxodonta africana, Monodelphis domestica, Macaca mulatta, Oryctolagus cuniculus, Otolemur garnettii, Pongo pygmaeus, Pan troglodytes, Sus scrofa, 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 9 annotation(s) with p-values below 0.001.
JASPAR: (0 annot.): none
TRANSFAC: (9 annot.): Lhx3a(8.01E-05) ,    HNF-1alpha(1.61E-04) ,    S8(2.63E-04) ,    HOXA5(3.21E-04) ,    POU6F1_(c2)(4.70E-04) ...
ORegAnno: (0 annot.): none
Modules
(Co-occurring motif patterns)		 Annotation-based:
25 (FOXJ2__Lhx3a)     96 (HNF-3__S8)     111 (CUTL1__HNF-1alpha)     112 (CUTL1__S8)     152 (HNF-1alpha__IRF-7A)     180 (CUTL1__HOXA5)     185 (HNF-1alpha__HNF-3)     204 (HOXA5__HOXA5)     210 (FOXJ2__HNF-1alpha)     235 (Hlf__Lhx3a)     281 (Nkx3-1__S8)     339 (HOXA5__S8)     349 (HNF-1alpha__Hlf)     379 (Evi-1__HNF-1alpha)     463 (Evi-1__Lhx3a)     464 (Evi-1__S8)     601 (IRF-7A__S8)     658 (CUTL1__Lhx3a)     691 (HOXA5__Nkx3-1)     716 (HOXA5__IRF-7A)     846 (FOXD3__HNF-1alpha)     902 (FOXD3__S8)     940 (HNF-1alpha__Nkx3-1)     1025 (HOXA5__Lhx3a)     1062 (HNF-1alpha__HOXA5)     1079 (FOXJ2__HOXA5)     1147 (HNF-1alpha__S8)     1183 (FOXJ2__S8)     1238 (HNF-3__HOXA5)     1254 (HNF-1alpha__HNF-1alpha)     1299 (Hlf__S8)     1305 (HNF-3__Lhx3a)     1339 (FOXD3__HOXA5)     1355 (HOXA5__Hlf)     1366 (Lhx3a__Nkx3-1)     1411 (HNF-1alpha__Lhx3a)     1439 (Evi-1__HOXA5)    

No 'de novo' modules exist in this database.

Sequence Conservation
Sequence logo (+)motif (-)motif
Consensus sequence AATATTTAyTTs wAArTAAATATT
Position frequency matrix
1 2 3 4 5 6 7 8 9 10 11 12
A 21 18 0 19 7 7 0 19 4 5 0 8
C 0 3 0 0 0 0 0 0 11 0 1 0
G 0 0 0 1 0 0 0 2 0 0 0 3
T 0 0 21 1 14 14 21 0 6 16 20 10
A A T A T T T A y T T w
1 2 3 4 5 6 7 8 9 10 11 12
A 10 20 16 6 0 21 14 14 1 21 0 0
C 3 0 0 0 2 0 0 0 1 0 0 0
G 0 1 0 11 0 0 0 0 0 0 3 0
T 8 0 5 4 19 0 7 7 19 0 18 21
w A A r T A A A T A T T

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
ENSMUSG00000070362 Target Mus musculus chr3:112,976,115-112,976,126 + AATAATTAATTT – AAATTAATTATT
ENSMUSG00000070362_CFAM Orthologue Canis familiaris chrUn:46,712,572-46,712,583 – AATAAATACATA + TATGTATTTATT
ENSMUSG00000070362_CHOF Orthologue Choloepus hoffmanni ENSMUSG00000070362_CHOF:147-158 – ACTATTTATATT + AATATAAATAGT
ENSMUSG00000070362_CJAC Orthologue Callithrix jacchus ENSMUSG00000070362_CJAC:155-166 + AATATTTACTTT – AAAGTAAATATT
ENSMUSG00000070362_DNOV Orthologue Dasypus novemcinctus scaffold_140518:1,896-1,907 + AATATTTGCTTT – AAAGCAAATATT
ENSMUSG00000070362_ECAB Orthologue Equus caballus ENSMUSG00000070362_ECAB:354-365 + AATATTTACTTA – TAAGTAAATATT
ENSMUSG00000070362_ETEL Orthologue Echinops telfairi scaffold_200667:3,258-3,269 + AATATTTATTTT – AAAATAAATATT
ENSMUSG00000070362_FRUB Orthologue Fugu rubripes chrUn:224,060,798-224,060,809 + AATATTTACATT – AATGTAAATATT
ENSMUSG00000070362_GGAL Orthologue Gallus gallus chr8:11,425,079-11,425,090 + AATATTTGATTA – TAATCAAATATT
ENSMUSG00000070362_HSAP Orthologue Homo sapiens chr1:104,005,017-104,005,028 – AATAAATACTTG + CAAGTATTTATT
ENSMUSG00000070362_LAFR Orthologue Loxodonta africana scaffold_61363:624-635 + AATAATTATTTA – TAAATAATTATT
ENSMUSG00000070362_MDOM Orthologue Monodelphis domestica scaffold_0:14,539,891-14,539,902 + AATATTTATTTG – CAAATAAATATT
ENSMUSG00000070362_MMUL Orthologue Macaca mulatta SCAFFOLD812:37,504-37,515 + AATATTTACTTT – AAAGTAAATATT
ENSMUSG00000070362_OCUN Orthologue Oryctolagus cuniculus scaffold_155133:12,206-12,217 + AATATTTACTTT – AAAGTAAATATT
ENSMUSG00000070362_OGAR Orthologue Otolemur garnettii ENSMUSG00000070362_OGAR:258-269 – ACTATTTATACT + AGTATAAATAGT
ENSMUSG00000070362_PPYG Orthologue Pongo pygmaeus ENSMUSG00000070362_PPYG:209-220 – ACTATTTATATT + AATATAAATAGT
ENSMUSG00000070362_PTRO Orthologue Pan troglodytes chr1:103,080,624-103,080,635 – AATAAATACTTG + CAAGTATTTATT
ENSMUSG00000070362_SSCR Orthologue Sus scrofa ENSMUSG00000070362_SSCR:107-118 – AATAAATACTTA + TAAGTATTTATT
ENSMUSG00000070362_TBEL Orthologue Tupaia belangeri ENSMUSG00000070362_TBEL:501-512 – AATTTATAATTA + TAATTATAAATT
ENSMUSG00000070362_TNIG Orthologue Tetraodon nigroviridis 15_random:2,106,297-2,106,308 + AATATATAATTA – TAATTATATATT
ENSMUSG00000070362_XTRO Orthologue Xenopus tropicalis scaffold_466:404,563-404,574 – AATGAATACTTA + TAAGTATTCATT

Questions or comments: cisred@bcgsc.ca