Region for Gene 2RSSE.1

This page describes one promoter-based search region.

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.

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 C.elegans genome assembly from Jan 2007. (UCSC ce4, WS170, Ensembl v45) 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.

Showing 38 out of 38 atomic motifs.

Group(s) crtCele#(name) [p-value]	Motif craCele#	Discovery p-value	Location	Width	(+)motif	(-)motif
0 annotated groups 0 'de novo' group(s)	1	5.84E-01	CHROMOSOME_II:15,266,445-15,266,458	14	TACnAmTAATmTTr	yAAkATTAkTnGTA
0 annotated groups 0 'de novo' group(s)	2	6.52E-01	CHROMOSOME_II:15,266,451-15,266,464	14	yAAkATTAGTCTTA	TAAGACTAATmTTr
0 annotated groups 0 'de novo' group(s)	3	8.91E-01	CHROMOSOME_II:15,266,503-15,266,514	12	AysnCTAATmTT	AAkATTAGnwrT
0 annotated groups 0 'de novo' group(s)	4	8.66E-01	CHROMOSOME_II:15,266,540-15,266,553	14	CwnTAwyyGTGAwA	TsTCACrrsTAnsG
1 annotated group(s): 30003 (15492775-EARLY-1) [1.26E-05] 3 'de novo' group(s) 4, 77, 566	5	7.53E-01	CHROMOSOME_II:15,266,582-15,266,595	14	AmAnTCTGCGTCkC	GmGACGCAGAnTkT
0 annotated groups 0 'de novo' group(s)	6	7.56E-01	CHROMOSOME_II:15,266,608-15,266,624	17	AnAnkCnTACTGGTTTs	wAAACCAGTAnGmnTnT
0 annotated groups 1 'de novo' group(s) 73	7	2.24E-01	CHROMOSOME_II:15,266,631-15,266,638	8	CCGCCAAC	GTTGGCGG
0 annotated groups 2 'de novo' group(s) 175, 1156	9	7.12E-01	CHROMOSOME_II:15,266,709-15,266,720	12	nACGAGGCGAGC	GCTCGCCTCGTn
0 annotated groups 2 'de novo' group(s) 175, 1156	8	9.21E-01	CHROMOSOME_II:15,266,710-15,266,723	14	mCGmrGCGCnnyGC	GCrnnGCGCykCGk
0 annotated groups 0 'de novo' group(s)	10	1.40E-01	CHROMOSOME_II:15,266,719-15,266,726	8	CCCGCCAA	TTGGCGGG
0 annotated groups 0 'de novo' group(s)	11	8.58E-01	CHROMOSOME_II:15,266,737-15,266,750	14	TACnAAArATATCA	TGATATyTTTnGTA
0 annotated groups 0 'de novo' group(s)	12	9.56E-01	CHROMOSOME_II:15,267,196-15,267,207	12	AGyTGGCGGGTA	TACCCGCCArCT
0 annotated groups 0 'de novo' group(s)	13	1.99E-01	CHROMOSOME_II:15,267,399-15,267,414	16	yATAATTACTTAATTA	TAATTAAGTAATTATr
2 annotated group(s): 40066 (Egr-1) [5.07E-06] 50073 (RREB-1) [1.71E-05] 2 'de novo' group(s) 642, 3118	14	8.89E-01	CHROMOSOME_II:15,267,438-15,267,457	20	GnrnnACmACCATsACAACn	nGTTGTwATGGTkGTnnynC
1 annotated group(s): 50062 (NRF-2) [8.71E-05] 0 'de novo' group(s)	15	6.95E-01	CHROMOSOME_II:15,267,484-15,267,495	12	nTnCTTCGTCGT	ACGACGAAGnAn
0 annotated groups 3 'de novo' group(s) 343, 3053, 1849	16	9.42E-01	CHROMOSOME_II:15,267,556-15,267,569	14	AGATTAGTGGTAGC	GCTACCACTAATCT
1 annotated group(s): 40167 (PPAR-alpha) [1.52E-06] 0 'de novo' group(s)	17	8.27E-01	CHROMOSOME_II:15,267,829-15,267,842	14	AnArkyATACnGsT	AwCnGTATrmyTnT
0 annotated groups 0 'de novo' group(s)	18	8.49E-01	CHROMOSOME_II:15,267,883-15,267,898	16	AnnnTGGTGGTAATkG	CmATTACCACCAnnnT
0 annotated groups 0 'de novo' group(s)	19	9.39E-01	CHROMOSOME_II:15,268,022-15,268,033	12	knTTAGTGGTwk	msACCACTAAnm
2 annotated group(s): 50101 (c-REL) [5.63E-05] 50107 (p65) [9.42E-05] 0 'de novo' group(s)	20	7.60E-02	CHROMOSOME_II:15,268,102-15,268,118	17	TnCAGTTGGCGGGTATT	AATACCCGCCAACTGnA
0 annotated groups 2 'de novo' group(s) 35, 64	21	2.18E-01	CHROMOSOME_II:15,268,117-15,268,146	30	TTCCAAGATTAGTGGTA...	AnGAGGATrCAGCTACC...
0 annotated groups 0 'de novo' group(s)	22	5.50E-01	CHROMOSOME_II:15,268,154-15,268,165	12	GCAnCACCATCA	TGATGGTGnTGC
1 annotated group(s): 40167 (PPAR-alpha) [4.39E-06] 0 'de novo' group(s)	23	6.74E-01	CHROMOSOME_II:15,268,161-15,268,184	24	CnyCrCCrCCACsACsA...	nTwGTwGTwGTwGTGGy...
1 annotated group(s): 40167 (PPAR-alpha) [4.39E-06] 4 'de novo' group(s) 43, 459, 795, 1716	25	6.66E-01	CHROMOSOME_II:15,268,178-15,268,194	17	CCrCCACGACGACGnCn	nGnCGTCGTCGTGGyGG
1 annotated group(s): 40167 (PPAR-alpha) [4.39E-06] 1 'de novo' group(s) 795	24	4.74E-01	CHROMOSOME_II:15,268,181-15,268,192	12	CCGCCnCGACGm	kCGTCGnGGCGG
0 annotated groups 1 'de novo' group(s) 65	26	6.42E-01	CHROMOSOME_II:15,268,191-15,268,202	12	GCnCGmCTCGTn	nACGAGkCGnGC
0 annotated groups 0 'de novo' group(s)	27	9.20E-01	CHROMOSOME_II:15,268,205-15,268,224	20	GTCGCCGCAGCAnCAnCAnC	GnTGnTGnTGCTGCGGCGAC
0 annotated groups 2 'de novo' group(s) 69, 293	28	7.63E-01	CHROMOSOME_II:15,268,224-15,268,237	14	CmCCATCAkCmnCG	CGnkGmTGATGGkG
0 annotated groups 6 'de novo' group(s) 7, 91, 578, 640, 1486, 2478	29	7.48E-01	CHROMOSOME_II:15,268,232-15,268,259	28	nCCGksmrTCACGACGw...	TkrArACGACGsCGTCG...
3 annotated group(s): 40217 (ZID) [4.05E-06] 40117 (LXR-alpha) [7.38E-06] 40167 (PPAR-alpha) [8.56E-06] 2 'de novo' group(s) 24, 96	30	8.48E-01	CHROMOSOME_II:15,268,284-15,268,300	17	nynCCmCCnyCwCCACC	GGTGGsGrnGGkGGnrn
5 annotated group(s): 40092 (HIF-1) [6.63E-07] 40115 (Lmo2) [1.26E-06] 40167 (PPAR-alpha) [8.56E-06] ... 15 'de novo' group(s) 7, 11, 16, 91, 578, 624, 762, 804, 1019, 1486, 1541, 2478, 2713, 2809, 1817	31	4.17E-01	CHROMOSOME_II:15,268,298-15,268,366	69	nCCGCCrCsACGACGAC...	GCkrCGCnGnGGnTGnT...
2 annotated group(s): 40092 (HIF-1) [6.63E-07] 50007 (Androgen) [9.48E-05] 5 'de novo' group(s) 16, 91, 762, 1541, 2713	32	4.59E-01	CHROMOSOME_II:15,268,333-15,268,346	14	CrCkkCGCCGCnGC	GCnGCGGCGmmGyG
1 annotated group(s): 40092 (HIF-1) [6.63E-07] 2 'de novo' group(s) 91, 762	33	5.24E-01	CHROMOSOME_II:15,268,335-15,268,344	10	CGkCGCAGCG	CGCTGCGmCG
1 annotated group(s): 40092 (HIF-1) [6.63E-07] 3 'de novo' group(s) 91, 762, 1541	34	8.12E-02	CHROMOSOME_II:15,268,335-15,268,346	12	CGTCGCCGCAGC	GCTGCGGCGACG
1 annotated group(s): 40092 (HIF-1) [6.63E-07] 3 'de novo' group(s) 91, 762, 1541	35	1.95E-01	CHROMOSOME_II:15,268,335-15,268,348	14	CGTCGCCGCAGCAC	GTGCTGCGGCGACG
0 annotated groups 0 'de novo' group(s)	39	6.97E-02	CHROMOSOME_II:15,268,340-15,268,349	10	CCGCAGCACC	GGTGCTGCGG
1 annotated group(s): 50091 (Tal1beta-E47S) [8.78E-05] 2 'de novo' group(s) 400, 1282	41	4.52E-01	CHROMOSOME_II:15,268,360-15,268,373	14	GCmnCGkCGCAGCG	CGCTGCGmCGnkGC
0 annotated groups 2 'de novo' group(s) 400, 924	43	3.16E-01	CHROMOSOME_II:15,268,361-15,268,375	15	CrTCGTCGTrGCGGC	GCCGCyACGACGAyG