cisRED: cis-regulatory element database

cisRED > C.elegans 4 > gene. F13G3.1 > craCele49326

Motif craCele49326

More information about this gene at Ensembl.org

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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	craCele49326
Discovery p-value	4.52E-01
Motif location	CHROMOSOME_I: 7,290,089-7,290,095 (+) (7 bp)
Search region location	CHROMOSOME_I: 7,289,770-7,291,269 (+) (1,500 bp)
Assembly	C.elegans, Ensembl v45 (WS170)
Found in	4 species: C elegans, C remanei, C japonica, C briggsae
Found with	MotifSampler
'De Novo' motif group ID	OPTICS/BOSS not in a cluster
Similar to (annotation p-value)	There are 0 annotation(s) with p-values below 0.001. JASPAR: (0 annot.): none TRANSFAC: (0 annot.): none ORegAnno: (0 annot.): none
Modules (Co-occurring motif patterns)	No annotation-based modules exist in this database. No 'de novo' modules exist in this database.

Sequence Conservation

Sequence logo

(+)motif

(-)motif

Consensus sequence

nCCTmCC

GGkAGGn

Position frequency matrix

	1	2	3	4	5	6	7
A	1	0	0	0	2	0	0
C	1	4	4	0	2	4	4
G	1	0	0	0	0	0	0
T	1	0	0	4	0	0	0
	n	C	C	T	m	C	C

Transfac

Jaspar

CSV

	1	2	3	4	5	6	7
A	0	0	0	4	0	0	1
C	0	0	0	0	0	0	1
G	4	4	2	0	4	4	1
T	0	0	2	0	0	0	1
	G	G	k	A	G	G	n

Transfac

Jaspar

CSV

Ensembl gene ID	Type	Species	Position	Std	(+)Sequence	Std	(-)Sequence
Site Sequence Stack
F13G3.1	Target	C elegans	CHROMOSOME_I:7,290,089-7,290,095	+	GCCTACC	–	GGTAGGC
F13G3.1_Crem_c1	Orthologue	C remanei	supercontigs.fa.Contig209:24,322-24,328	+	ACCTCCC	–	GGGAGGT
F13G3.1_Cjap_c1	Orthologue	C japonica	supercontigs.fa.Contig30:91,383-91,389	+	CCCTACC	–	GGTAGGG
F13G3.1_Cbri_c1	Orthologue	C briggsae	assembly.fasta.chrII:1,987,188-1,987,194	+	TCCTCCC	–	GGGAGGA

Export Site Sequences Stack