Region for Gene B0034.3c

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 83 out of 83 atomic motifs.

Group(s) crtCele#(name) [p-value]	Motif craCele#	Discovery p-value	Location	Width	(+)motif	(-)motif
0 annotated groups 2 'de novo' group(s) 661, 1655	752	7.43E-02	CHROMOSOME_II:5,947,265-5,947,278	14	AGAACATTCTGGAA	TTCCAGAATGTTCT
0 annotated groups 1 'de novo' group(s) 1655	741	1.00E-08	CHROMOSOME_II:5,947,266-5,947,281	16	TTCAGAACATTCTGGA	TCCAGAATGTTCTGAA
0 annotated groups 0 'de novo' group(s)	751	1.00E-08	CHROMOSOME_II:5,947,267-5,947,272	6	TTCTGG	CCAGAA
0 annotated groups 0 'de novo' group(s)	746	1.00E-08	CHROMOSOME_II:5,947,270-5,947,277	8	GAACATTC	GAATGTTC
0 annotated groups 0 'de novo' group(s)	740	4.74E-01	CHROMOSOME_II:5,947,292-5,947,303	12	TCCGAATCTGAT	ATCAGATTCGGA
0 annotated groups 0 'de novo' group(s)	739	9.39E-01	CHROMOSOME_II:5,947,300-5,947,314	15	rGCTTCAGAATTCTk	mAGAATTCTGAAGCy
0 annotated groups 0 'de novo' group(s)	738	7.73E-01	CHROMOSOME_II:5,947,316-5,947,328	13	nnATTCTATGTAT	ATACATAGAATnn
0 annotated groups 0 'de novo' group(s)	737	7.91E-01	CHROMOSOME_II:5,947,325-5,947,334	10	CTAGATGAGG	CCTCATCTAG
0 annotated groups 0 'de novo' group(s)	736	3.72E-01	CHROMOSOME_II:5,947,341-5,947,354	14	TCTGATTTAATCAA	TTGATTAAATCAGA
0 annotated groups 0 'de novo' group(s)	735	8.22E-01	CHROMOSOME_II:5,947,363-5,947,376	14	TCAGAATTCTGCyC	GrGCAGAATTCTGA
0 annotated groups 0 'de novo' group(s)	734	4.74E-01	CHROMOSOME_II:5,947,374-5,947,385	12	TCCAGAATGTTC	GAACATTCTGGA
0 annotated groups 0 'de novo' group(s)	733	1.00E-08	CHROMOSOME_II:5,947,390-5,947,395	6	ATACAT	ATGTAT
0 annotated groups 0 'de novo' group(s)	732	9.56E-01	CHROMOSOME_II:5,947,402-5,947,413	12	TCTCwAGATGAG	CTCATCTsGAGA
0 annotated groups 0 'de novo' group(s)	731	6.90E-01	CHROMOSOME_II:5,947,412-5,947,427	16	kTCwGAACwkTCTGGm	kCCAGAmsGTTCsGAm
0 annotated groups 0 'de novo' group(s)	730	7.12E-01	CHROMOSOME_II:5,947,424-5,947,435	12	ATCAAGGTGnnw	snnCACCTTGAT
0 annotated groups 3 'de novo' group(s) 42, 75, 2577	729	1.40E-01	CHROMOSOME_II:5,947,440-5,947,482	43	TnGGAATGGCCTTTTGG...	GmCTCATCTAGnGAATA...
0 annotated groups 3 'de novo' group(s) 389, 638, 1729	728	2.96E-01	CHROMOSOME_II:5,947,484-5,947,495	12	kCCACGTCTTCT	AGAAGACGTGGm
0 annotated groups 0 'de novo' group(s)	727	3.68E-01	CHROMOSOME_II:5,947,504-5,947,520	17	TTCCTCyTTCGTCCACT	AGTGGACGAArGAGGAA
2 annotated group(s): 50014 (Bsap) [3.62E-05] 30007 (CHE-1) [7.36E-05] 0 'de novo' group(s)	726	1.56E-01	CHROMOSOME_II:5,947,524-5,947,531	8	TTsGCTTC	GAAGCwAA
1 annotated group(s): 50014 (Bsap) [3.62E-05] 0 'de novo' group(s)	725	2.18E-01	CHROMOSOME_II:5,947,533-5,947,562	30	TCAAACCATTCTCCTCC...	TAGGAGAAGAGGTGGAG...
1 annotated group(s): 50038 (Gfi) [8.18E-05] 4 'de novo' group(s) 7, 75, 157, 1211	724	8.77E-02	CHROMOSOME_II:5,947,555-5,947,587	33	nGyCGTCCATCCGAATC...	TGGTTTGATTAAATCAG...
0 annotated groups 2 'de novo' group(s) 25, 431	723	9.43E-01	CHROMOSOME_II:5,947,587-5,947,614	28	ynTnnnGnnnCAynkAG...	TACTkAGAATGCTmnrT...
0 annotated groups 0 'de novo' group(s)	722	6.60E-01	CHROMOSOME_II:5,947,613-5,947,627	15	TkCnCACTCTTCynn	nnrGAAGAGTGnGmA
1 annotated group(s): 40205 (TFIIA) [7.59E-06] 1 'de novo' group(s) 3039	721	7.41E-02	CHROMOSOME_II:5,947,636-5,947,654	19	ACAACAAAAACATCTTCTC	GAGAAGATGTTTTTGTTGT
0 annotated groups 0 'de novo' group(s)	720	1.57E-01	CHROMOSOME_II:5,947,657-5,947,669	13	AAGCTGAAGAAGn	nCTTCTTCAGCTT
1 annotated group(s): 50009 (Brachyury) [7.68E-05] 1 'de novo' group(s) 2910	719	5.91E-01	CHROMOSOME_II:5,947,666-5,947,681	16	nAGAAGAAGAAGAAGn	nCTTCTTCTTCTTCTn
1 annotated group(s): 50073 (RREB-1) [3.66E-05] 1 'de novo' group(s) 60	718	7.33E-01	CHROMOSOME_II:5,947,686-5,947,698	13	nTGGyCnkTTGGy	rCCAAmnGrCCAn
0 annotated groups 0 'de novo' group(s)	717	2.80E-01	CHROMOSOME_II:5,947,696-5,947,709	14	TTTCGTAACGACkG	CmGTCGTTACGAAA
0 annotated groups 0 'de novo' group(s)	716	4.00E-01	CHROMOSOME_II:5,947,735-5,947,746	12	GAAGAGkGnGCA	TGCnCmCTCTTC
0 annotated groups 0 'de novo' group(s)	715	1.26E-01	CHROMOSOME_II:5,947,741-5,947,754	14	AAGAAGAAGAAGAA	TTCTTCTTCTTCTT
1 annotated group(s): 50074 (RXR-VDR) [5.96E-05] 0 'de novo' group(s)	714	6.07E-01	CHROMOSOME_II:5,947,788-5,947,807	20	nnGGnnAGATGTTTATGwGr	yCsCATAAACATCTnnCCnn
0 annotated groups 0 'de novo' group(s)	713	1.40E-01	CHROMOSOME_II:5,947,806-5,947,813	8	CATTCTGG	CCAGAATG
0 annotated groups 1 'de novo' group(s) 775	712	5.91E-01	CHROMOSOME_II:5,947,810-5,947,822	13	CTCATCwTTCnnn	nnnGAAsGATGAG
0 annotated groups 0 'de novo' group(s)	711	4.15E-01	CHROMOSOME_II:5,947,832-5,947,847	16	TCTATCATTCTCAGwA	TsCTGAGAATGATAGA
0 annotated groups 0 'de novo' group(s)	710	3.52E-01	CHROMOSOME_II:5,947,835-5,947,842	8	CATTCTsG	CwAGAATG
1 annotated group(s): 50018 (CREB) [4.38E-05] 0 'de novo' group(s)	709	3.83E-01	CHROMOSOME_II:5,947,844-5,947,858	15	GTCACGAnGrATCTA	TAGATyCnTCGTGAC
0 annotated groups 0 'de novo' group(s)	708	7.73E-01	CHROMOSOME_II:5,947,900-5,947,913	14	ATGTwTTCACTnTn	nAnAGTGAAsACAT
1 annotated group(s): 50072 (RORalfa-2) [3.98E-05] 0 'de novo' group(s)	707	2.29E-01	CHROMOSOME_II:5,947,906-5,947,919	14	GATTTCCTGTTTTy	rAAAACAGGAAATC
1 annotated group(s): 40090 (HES-1) [5.33E-06] 1 'de novo' group(s) 50	706	7.85E-01	CHROMOSOME_II:5,947,939-5,947,952	14	nATCGCTnGwkGAG	CTCmsCnAGCGATn
0 annotated groups 0 'de novo' group(s)	705	4.94E-01	CHROMOSOME_II:5,947,992-5,947,999	8	CTTnTCrC	GyGAnAAG
0 annotated groups 0 'de novo' group(s)	704	5.55E-01	CHROMOSOME_II:5,947,998-5,948,009	12	CnnCTTCTCTCT	AGAGAGAAGnnG
0 annotated groups 0 'de novo' group(s)	703	7.84E-01	CHROMOSOME_II:5,948,004-5,948,015	12	GyAGCGCCACTT	AAGTGGCGCTrC
0 annotated groups 0 'de novo' group(s)	702	7.12E-01	CHROMOSOME_II:5,948,012-5,948,023	12	TCCAGAATGTTC	GAACATTCTGGA
0 annotated groups 3 'de novo' group(s) 53, 376, 773	700	9.10E-01	CHROMOSOME_II:5,948,022-5,948,035	14	TCCAGAATGTTCTG	CAGAACATTCTGGA
0 annotated groups 2 'de novo' group(s) 53, 67	701	7.26E-01	CHROMOSOME_II:5,948,026-5,948,039	14	nTyGGATGGACGGC	GCCGTCCATCCrAn
0 annotated groups 1 'de novo' group(s) 2050	699	2.95E-01	CHROMOSOME_II:5,948,036-5,948,052	17	nnGCATCAGATTTCTTn	nAAGAAATCTGATGCnn
0 annotated groups 0 'de novo' group(s)	698	8.56E-01	CHROMOSOME_II:5,948,046-5,948,060	15	TGGCCTTTTGGCATT	AATGCCAAAAGGCCA
0 annotated groups 1 'de novo' group(s) 105	697	5.35E-01	CHROMOSOME_II:5,948,056-5,948,065	10	TCGCTnCrnn	nnyGnAGCGA
0 annotated groups 0 'de novo' group(s)	696	9.06E-02	CHROMOSOME_II:5,948,064-5,948,077	14	GGGCCAGCTCATTC	GAATGAGCTGGCCC
0 annotated groups 0 'de novo' group(s)	695	5.65E-02	CHROMOSOME_II:5,948,074-5,948,086	13	GCACAAATTGGGC	GCCCAATTTGTGC
2 annotated group(s): 40092 (HIF-1) [8.60E-06] 40092 (HIF-1) [9.88E-06] 2 'de novo' group(s) 27, 2050	694	6.50E-01	CHROMOSOME_II:5,948,084-5,948,111	28	CTwCkynCTGAAATATG...	TGCnnGArGATCATATT...
0 annotated groups 0 'de novo' group(s)	693	9.04E-02	CHROMOSOME_II:5,948,117-5,948,123	7	nGAAGAG	CTCTTCn
0 annotated groups 0 'de novo' group(s)	692	4.03E-01	CHROMOSOME_II:5,948,128-5,948,142	15	TTTCTTCTmCnACTT	AAGTnGkAGAAGAAA
0 annotated groups 0 'de novo' group(s)	691	1.90E-01	CHROMOSOME_II:5,948,154-5,948,170	17	TTCTTCTTCTTCTTnyT	ArnAAGAAGAAGAAGAA
0 annotated groups 0 'de novo' group(s)	690	4.39E-01	CHROMOSOME_II:5,948,173-5,948,186	14	ACACACAAGTTTAG	CTAAACTTGTGTGT
1 annotated group(s): 50048 (Hen-1) [9.03E-05] 2 'de novo' group(s) 22, 131	689	6.28E-01	CHROMOSOME_II:5,948,180-5,948,199	20	nnnCnArCTGACCACACAnA	TnTGTGTGGTCAGyTnGnnn
0 annotated groups 0 'de novo' group(s)	688	7.32E-01	CHROMOSOME_II:5,948,209-5,948,216	8	nCAGAmTG	CAkTCTGn
0 annotated groups 2 'de novo' group(s) 25, 283	687	1.00E-01	CHROMOSOME_II:5,948,225-5,948,246	22	AAATAATTGTAAATGTA...	TGrCATACATTTACAAT...
1 annotated group(s): 40045 (COUP) [6.35E-06] 0 'de novo' group(s)	686	4.70E-01	CHROMOSOME_II:5,948,243-5,948,262	20	TmTGATCTwmyCrCACAAAT	ATTTGTGyGrksAGATCAkA
0 annotated groups 0 'de novo' group(s)	685	8.56E-01	CHROMOSOME_II:5,948,264-5,948,273	10	CAnGATGAGT	ACTCATCnTG
0 annotated groups 0 'de novo' group(s)	684	5.15E-01	CHROMOSOME_II:5,948,319-5,948,328	10	ATACATnTAC	GTAnATGTAT
0 annotated groups 0 'de novo' group(s)	683	1.40E-01	CHROMOSOME_II:5,948,346-5,948,353	8	GGATGGAC	GTCCATCC
0 annotated groups 0 'de novo' group(s)	682	7.03E-01	CHROMOSOME_II:5,948,366-5,948,379	14	rAAGACyCTTTGCC	GGCAAAGrGTCTTy
0 annotated groups 0 'de novo' group(s)	681	5.78E-01	CHROMOSOME_II:5,948,396-5,948,409	14	ATTTACmATTrTTT	AAAyAATkGTAAAT
1 annotated group(s): 50007 (Androgen) [1.07E-05] 0 'de novo' group(s)	680	9.09E-01	CHROMOSOME_II:5,948,427-5,948,440	14	CTTCnnGTGCCyyy	rrrGGCACnnGAAG
0 annotated groups 0 'de novo' group(s)	679	5.84E-01	CHROMOSOME_II:5,948,464-5,948,477	14	AmAAAmAGGAnATC	GATnTCCTkTTTkT
0 annotated groups 0 'de novo' group(s)	678	3.69E-01	CHROMOSOME_II:5,948,487-5,948,494	8	CGCCGCTC	GAGCGGCG
1 annotated group(s): 50065 (PPARgamma-RXRal) [5.95E-05] 0 'de novo' group(s)	677	8.38E-01	CHROMOSOME_II:5,948,500-5,948,511	12	CAGAATTCTGCT	AGCAGAATTCTG
1 annotated group(s): 50074 (RXR-VDR) [8.09E-05] 1 'de novo' group(s) 73	676	9.42E-01	CHROMOSOME_II:5,948,533-5,948,546	14	CAGsTnGTCGCTCC	GGAGCGACnAwCTG
0 annotated groups 0 'de novo' group(s)	675	5.54E-01	CHROMOSOME_II:5,948,549-5,948,560	12	CCTCwTCnAGkG	CmCTnGAsGAGG
0 annotated groups 0 'de novo' group(s)	674	1.02E-01	CHROMOSOME_II:5,948,567-5,948,572	6	AwGTAT	ATACsT
0 annotated groups 3 'de novo' group(s) 661, 906, 1655	673	1.36E-01	CHROMOSOME_II:5,948,577-5,948,606	30	ACTnGTATTCCAGAATG...	mACTTACCACGAACATT...
0 annotated groups 0 'de novo' group(s)	669	4.60E-02	CHROMOSOME_II:5,948,586-5,948,597	12	CCAGAATGTTCG	CGAACATTCTGG
0 annotated groups 1 'de novo' group(s) 1655	666	1.00E-08	CHROMOSOME_II:5,948,587-5,948,598	12	TCCAGAATGTTC	GAACATTCTGGA
0 annotated groups 0 'de novo' group(s)	667	1.00E-08	CHROMOSOME_II:5,948,592-5,948,597	6	CCAGAA	TTCTGG
0 annotated groups 0 'de novo' group(s)	665	3.40E-01	CHROMOSOME_II:5,948,611-5,948,628	18	AsnGCAGAATTCTGAAGC	GCTTCAGAATTCTGCnwT
1 annotated group(s): 40163 (POU1F1) [2.02E-06] 0 'de novo' group(s)	664	8.38E-01	CHROMOSOME_II:5,948,630-5,948,647	18	ATnnATTTACAmTTATTT	AAATAAkTGTAAATnnAT
0 annotated groups 0 'de novo' group(s)	663	2.57E-01	CHROMOSOME_II:5,948,667-5,948,680	14	TCCAGAAGnAGCTn	nAGCTnCTTCTGGA
0 annotated groups 0 'de novo' group(s)	662	3.64E-01	CHROMOSOME_II:5,948,675-5,948,699	25	CCnGnAGCGACnAGCTG...	TCTGGAAGCAGCTnGTC...
1 annotated group(s): 40063 (E47) [9.32E-06] 0 'de novo' group(s)	661	2.90E-01	CHROMOSOME_II:5,948,696-5,948,709	14	CwCCATCTGCCCCG	CGGGGCAGATGGsG
1 annotated group(s): 40063 (E47) [9.32E-06] 0 'de novo' group(s)	660	6.37E-01	CHROMOSOME_II:5,948,706-5,948,720	15	TCTTCnnGTGCCyyC	GrrGGCACnnGAAGA
0 annotated groups 1 'de novo' group(s) 1050	659	9.06E-02	CHROMOSOME_II:5,948,726-5,948,739	14	AAGCAGCGCCACTT	AAGTGGCGCTGCTT
0 annotated groups 3 'de novo' group(s) 57, 146, 1131	658	1.61E-01	CHROMOSOME_II:5,948,745-5,948,764	20	wAAGGAAGGGCGCGAGAAAA	TTTTCTCGCGCCCTTCCTTs