cisRED: cis-regulatory element database

cisRED > Rat 1.1 > gene. ENSRNOG00000000467

Region for Gene ENSRNOG00000000467 (Uniprot/SPTREMBL: Ring1)

This page describes one promoter-based search region.

Page Contents

Overview
Genomic Context
Image of Motifs and Modules
Motifs Found in this Region

Search region overview
Search region location	chr20:4,966,921-4,968,677 (+) (1757 bp)
Assembly	Rat, Ensembl v22 (RGSC 3.1)
Gene name	Ring1
Ensembl gene ID	ENSRNOG00000000467
Gene description source	Uniprot/SPTREMBL
Modules (Co-occurring motif patterns)	No annotation-based modules were found. 13 'de novo' module(s)

Genomic Context: Rat genome assembly from Jun 2003. (UCSC rn3, RGSC 3.1, Ensembl v22)

The image shown below was created to provide context for this search region by showing a 100000 bp span of the genome, centered on this search region.

The first track shows the location of the search region in red.
The last track shows known gene locations in this 100000 bp span of the genome.

This promoter-based search region is located close to a particular gene of interest, described in the table below. Click on the gene id to open a page at ensembl.org with more information about this gene.

Target gene used to create this search region
Ensembl ID	ENSRNOG00000000467 (Ring1)
Ensembl Transcript ID	ENSRNOT00000000543
Gene location	chr20: 4,969,668-4,972,080 (+) (2,413 bp)
Distance from the region's midpoint to TSS	-1867

The distance from a cisred search region to a gene, is measured from the center of the search region to either the transcription termination site (TTS) or the transcription start site (TSS), whichever is closer.
A distance is negative if the TTS/TTS is downstream of the search region's center, relative to the gene's strand.
A distance is positive if the TTS/TTS is upstream of the search region's center, relative to the gene's strand.

A transcript's location is always reported relative to the positive strand.

Image of Motifs and Modules

The image shown below illustrates the location of the motifs and modules within this search region.
However, the number of modules in a region may exceed the genome browser's track limit. Thus, for each type of module (pattern), the text in the yellow box below indicates whether or not any modules of that type exist, and if so, whether or not all the modules of that type are displayed. (If it indicates that only the top 20 modules are displayed, this ranking is based on the number of instances of each module.)

User-specified filter settings do not affect the features displayed in the UCSC genome browser view.

About the patterns shown in this image:
There are no 'de novo' patterns to show.
There are no (TRANSFAC) annotation-based patterns to show.
There are no (JASPAR) annotation-based patterns to show.

Click on the image to view this region at UCSC.

This image uses the Rat genome assembly from Jun 2003. (UCSC rn3, RGSC 3.1, Ensembl v22) and contains a number of custom tracks followed by several UCSC tracks. The custom tracks show:

The long red and gray bar at the top shows the nominal 'search region' within which comparative genomics discovery methods were applied. Motif predictions were not made in coding exons and most types of repeats. In this database, the locations of masks applied to the search region are shown in gray.

The numbered brown blocks are 'atomic' motifs, i.e. conserved DNA sequence motifs that were identified by discovery methods and post-processing operations. Motifs are shaded to indicate the discovery p-value; a darker motif was more significant at the discovery stage.

Following the motif discovery stage, motifs were filtered by membership in co-occurring patterns, and patterns were ranked by genome-scale properties. Motifs instances that occur in highly-ranked putative regulatory modules may be more reliable predictions of functional genomic elements.

The connected sets of blue boxes are co-occurring patterns, i.e. putative regulatory modules. Modules are shaded to indicate the number of times that a pattern is found in the target genome; a darker module is associated with more search regions. An pattern is called either 'de novo' or annotation-based, depending on the type of groups that appear in the pattern. (see next point)

Before patterns (i.e. modules) can be identified from atomic motifs, groups of similar motifs must be found; modules are then identified as co-occurring 'group labels' that satisfy certain criteria. Such groups can be identified a) by annotating atomic motifs with known binding site resources from TRANSFAC, JASPAR or ORegAnno; or b) by 'de novo' clustering. Currently we show both types of patterns, but we consider annotation-based groups and patterns to be more reliable than 'de novo' groups and patterns. Work to improve genome-scale 'de novo' grouping is ongoing.

Motifs Found in this Region

The contents of the table below can be modified by changing your filter settings.
Currently, this table only contains motifs which:
+ have a discovery p-value < 0.25
+ were found using any of these algorithms: MotifSampler, Consensus.oops, Consensus.omops, Consensus.zmops, MEME.tcm, MEME.oops, MEME.zoops

Showing 63 out of 63 atomic motifs.

Group(s) crtRnor#(name) [p-value]	Motif craRnor#	Discovery p-value	Location	Width	(+)motif	(-)motif
0 annotated groups 0 'de novo' group(s)	27229	8.77E-03	chr20:4,966,938-4,966,947	10	TCCCCCACCC	GGGTGGGGGA
0 annotated groups 0 'de novo' group(s)	27297	8.77E-03	chr20:4,967,124-4,967,133	10	CmCCTCCCCC	GGGGGAGGkG
0 annotated groups 1 'de novo' group(s) 1996	27362	8.77E-03	chr20:4,967,126-4,967,133	8	CCTCCCCC	GGGGGAGG
0 annotated groups 1 'de novo' group(s) 2202	27428	8.77E-03	chr20:4,967,127-4,967,134	8	CTCCCCCC	GGGGGGAG
0 annotated groups 0 'de novo' group(s)	27485	1.59E-01	chr20:4,967,180-4,967,202	23	CmGGGCAACCCCCGCCG...	ACCCGGCGGCGGGGGTT...
0 annotated groups 1 'de novo' group(s) 504	27580	1.55E-01	chr20:4,967,255-4,967,267	13	CAGrGGGwGGssw	swwCCsCCCyCTG
0 annotated groups 0 'de novo' group(s)	27518	8.77E-03	chr20:4,967,259-4,967,268	10	GGGAGGGGAy	rTCCCCTCCC
0 annotated groups 1 'de novo' group(s) 2173	27614	8.77E-03	chr20:4,967,280-4,967,285	6	CCCCTC	GAGGGG
0 annotated groups 0 'de novo' group(s)	27677	8.77E-03	chr20:4,967,365-4,967,373	9	GCCCCATCC	GGATGGGGC
0 annotated groups 1 'de novo' group(s) 13210	27946	1.48E-01	chr20:4,967,414-4,967,435	22	CnnCCCymGTyCCCCCC...	AAGTAGGGGGGrACkrG...
0 annotated groups 1 'de novo' group(s) 2207	27739	8.77E-03	chr20:4,967,421-4,967,428	8	CCCCCACC	GGTGGGGG
0 annotated groups 1 'de novo' group(s) 1062	27811	8.77E-03	chr20:4,967,422-4,967,429	8	CCCCACCC	GGGTGGGG
0 annotated groups 1 'de novo' group(s) 5122	27873	8.77E-03	chr20:4,967,428-4,967,433	6	CCCTCC	GGAGGG
0 annotated groups 1 'de novo' group(s) 1250	27992	8.77E-03	chr20:4,967,443-4,967,452	10	kTCCCCTCCC	GGGAGGGGAm
0 annotated groups 1 'de novo' group(s) 390	28058	8.77E-03	chr20:4,967,444-4,967,455	12	mCCCCTCCCTTC	GAAGGGAGGGGk
0 annotated groups 1 'de novo' group(s) 504	28124	8.77E-03	chr20:4,967,445-4,967,456	12	CCCCTCCCTTCT	AGAAGGGAGGGG
0 annotated groups 1 'de novo' group(s) 680	28173	8.77E-03	chr20:4,967,446-4,967,455	10	CCCTCCCTTC	GAAGGGAGGG
0 annotated groups 0 'de novo' group(s)	28220	2.12E-01	chr20:4,967,460-4,967,475	16	CACCTTACAATAGCTG	CAGCTATTGTAAGGTG
0 annotated groups 0 'de novo' group(s)	28278	2.27E-02	chr20:4,967,470-4,967,481	12	TAGCTGCAGCCG	CGGCTGCAGCTA
0 annotated groups 1 'de novo' group(s) 3493	28322	1.85E-02	chr20:4,967,472-4,967,479	8	GCTGCAGC	GCTGCAGC
0 annotated groups 1 'de novo' group(s) 1151	28392	8.77E-03	chr20:4,967,486-4,967,493	8	GGGGTCGG	CCGACCCC
0 annotated groups 0 'de novo' group(s)	28442	8.77E-03	chr20:4,967,487-4,967,494	8	GGGTCGGA	TCCGACCC
0 annotated groups 1 'de novo' group(s) 1480	28500	8.77E-03	chr20:4,967,492-4,967,501	10	GGrTGGGGGr	yCCCCCAyCC
0 annotated groups 0 'de novo' group(s)	28573	8.77E-03	chr20:4,967,493-4,967,500	8	GrTGGGGG	CCCCCAyC
0 annotated groups 0 'de novo' group(s)	28645	8.77E-03	chr20:4,967,493-4,967,504	12	GATGGGGGGGAT	ATCCCCCCCATC
0 annotated groups 1 'de novo' group(s) 2121	28713	8.77E-03	chr20:4,967,495-4,967,502	8	TGGGGGGG	CCCCCCCA
0 annotated groups 1 'de novo' group(s) 2408	28765	8.77E-03	chr20:4,967,498-4,967,503	6	GGGGGA	TCCCCC
0 annotated groups 0 'de novo' group(s)	28849	8.77E-03	chr20:4,967,504-4,967,515	12	TTAGGGGAGGGG	CCCCTCCCCTAA
0 annotated groups 0 'de novo' group(s)	28914	8.77E-03	chr20:4,967,505-4,967,514	10	TAGGGGAGGG	CCCTCCCCTA
0 annotated groups 1 'de novo' group(s) 280	28971	8.77E-03	chr20:4,967,505-4,967,516	12	TAGGGGAGGGGG	CCCCCTCCCCTA
0 annotated groups 1 'de novo' group(s) 1996	29030	8.77E-03	chr20:4,967,507-4,967,514	8	GGGGAGGG	CCCTCCCC
0 annotated groups 1 'de novo' group(s) 725	29102	8.77E-03	chr20:4,967,527-4,967,534	8	GGGAATGG	CCATTCCC
0 annotated groups 1 'de novo' group(s) 504	29155	8.77E-03	chr20:4,967,565-4,967,576	12	AGAAGGGAGGGG	CCCCTCCCTTCT
0 annotated groups 1 'de novo' group(s) 680	29220	8.77E-03	chr20:4,967,566-4,967,575	10	GAAGGGAGGG	CCCTCCCTTC
0 annotated groups 1 'de novo' group(s) 390	29277	8.77E-03	chr20:4,967,566-4,967,577	12	GAAGGGAGGGGG	CCCCCTCCCTTC
0 annotated groups 1 'de novo' group(s) 1524	29336	8.77E-03	chr20:4,967,567-4,967,576	10	AAGGGAGGGG	CCCCTCCCTT
0 annotated groups 1 'de novo' group(s) 1573	29394	8.77E-03	chr20:4,967,568-4,967,577	10	rGGGAGGGGG	CCCCCTCCCy
0 annotated groups 1 'de novo' group(s) 1119	29443	8.77E-03	chr20:4,967,569-4,967,578	10	GGGAGGGGrC	GyCCCCTCCC
0 annotated groups 1 'de novo' group(s) 1150	29515	8.77E-03	chr20:4,967,571-4,967,578	8	GAGGGGGC	GCCCCCTC
0 annotated groups 1 'de novo' group(s) 479	29557	8.77E-03	chr20:4,967,688-4,967,697	10	GGGGTGGGGG	CCCCCACCCC
0 annotated groups 1 'de novo' group(s) 479	29621	8.77E-03	chr20:4,967,688-4,967,699	12	rGGTTkGGGGGC	GCCCCCmAACCy
0 annotated groups 1 'de novo' group(s) 9692	29686	1.52E-01	chr20:4,967,700-4,967,712	13	GAGGGGACCCACT	AGTGGGTCCCCTC
0 annotated groups 1 'de novo' group(s) 11581	29754	1.72E-01	chr20:4,967,718-4,967,732	15	CTTGTCCCAGAGAnA	TnTCTCTGGGACAAG
0 annotated groups 0 'de novo' group(s)	29778	7.40E-02	chr20:4,967,737-4,967,749	13	rCTsCCAGGGGGT	ACCCCCTGGwAGy
0 annotated groups 0 'de novo' group(s)	29976	1.38E-01	chr20:4,967,934-4,967,954	21	TsyCTssATTCCCCCTy...	AGGsrAGGGGGAATwwA...
0 annotated groups 1 'de novo' group(s) 2167	29842	8.77E-03	chr20:4,967,944-4,967,951	8	CCCCCTCC	GGAGGGGG
0 annotated groups 1 'de novo' group(s) 1573	29912	8.77E-03	chr20:4,967,944-4,967,953	10	CCCCCTCCCn	nGGGAGGGGG
0 annotated groups 0 'de novo' group(s)	30012	1.38E-01	chr20:4,967,970-4,967,987	18	GGTGyCCnCGCnnCCsCG	CGwGGnnGCGnGGrCACC
0 annotated groups 1 'de novo' group(s) 14872	30116	1.37E-01	chr20:4,968,028-4,968,046	19	ACGTCTCCGCCGGCGGGkG	CmCCCGCCGGCGGAGACGT
0 annotated groups 1 'de novo' group(s) 762	30050	2.27E-02	chr20:4,968,035-4,968,046	12	GGGCCGCGGCTC	GAGCCGCGGCCC
0 annotated groups 0 'de novo' group(s)	30137	2.27E-02	chr20:4,968,064-4,968,075	12	mTwmTCGAsTCT	AGAwTCGAksAk
0 annotated groups 1 'de novo' group(s) 762	30179	2.27E-02	chr20:4,968,110-4,968,121	12	GAGCCGCsGCCC	GGGCwGCGGCTC
0 annotated groups 1 'de novo' group(s) 479	30232	8.77E-03	chr20:4,968,118-4,968,129	12	GCCCCCmAACCy	rGGTTkGGGGGC
0 annotated groups 1 'de novo' group(s) 7771	30300	8.77E-03	chr20:4,968,162-4,968,167	6	GTCCCC	GGGGAC
0 annotated groups 1 'de novo' group(s) 5552	30355	8.77E-03	chr20:4,968,279-4,968,286	8	TGGGGAyC	GrTCCCCA
0 annotated groups 1 'de novo' group(s) 5122	30430	8.77E-03	chr20:4,968,295-4,968,300	6	GGAGGG	CCCTCC
0 annotated groups 1 'de novo' group(s) 5469	30504	8.77E-03	chr20:4,968,317-4,968,322	6	CTCTCC	GGAGAG
0 annotated groups 0 'de novo' group(s)	30549	8.77E-03	chr20:4,968,369-4,968,378	10	GGAGGGGGnn	nnCCCCCTCC
0 annotated groups 0 'de novo' group(s)	30624	1.40E-01	chr20:4,968,445-4,968,460	16	AGTCCTTATGTGGGCk	mGCCCACATAAGGACT
0 annotated groups 1 'de novo' group(s) 5116	30674	8.77E-03	chr20:4,968,473-4,968,478	6	CCCGGG	CCCGGG
0 annotated groups 0 'de novo' group(s)	30757	1.37E-01	chr20:4,968,553-4,968,572	20	CCCyyGGGGwCCnnrnGAAC	GTTCnynnGGsCCCCrrGGG
0 annotated groups 0 'de novo' group(s)	30724	2.33E-01	chr20:4,968,557-4,968,566	10	sGGGGwACCC	GGGTsCCCCw
0 annotated groups 1 'de novo' group(s) 10792	30794	8.77E-03	chr20:4,968,643-4,968,650	8	GGGCGGGG	CCCCGCCC