Region for Gene T09A5.2b

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 67 out of 67 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)	115456	5.26E-01	CHROMOSOME_II:7,840,850-7,840,859	10	AGAAyAGACT	AGTCTrTTCT
0 annotated groups 0 'de novo' group(s)	115457	4.74E-01	CHROMOSOME_II:7,840,873-7,840,884	12	TGTCrmTCGTTT	AAACGAkyGACA
2 annotated group(s): 50027 (EN-1) [5.33E-05] 50072 (RORalfa-2) [7.40E-05] 0 'de novo' group(s)	115458	2.74E-01	CHROMOSOME_II:7,840,885-7,840,895	11	wTTGTTGGTCA	TGACCAACAAs
2 annotated group(s): 50027 (EN-1) [5.33E-05] 50072 (RORalfa-2) [7.40E-05] 2 'de novo' group(s) 20, 3207	115459	8.78E-01	CHROMOSOME_II:7,840,891-7,840,913	23	GGTCACAAATAAywwAT...	AknATGATssrTTATTT...
0 annotated groups 1 'de novo' group(s) 8	115460	8.76E-01	CHROMOSOME_II:7,840,931-7,840,942	12	AGCAAACAACAs	wTGTTGTTTGCT
0 annotated groups 3 'de novo' group(s) 782, 2456, 1720	115461	7.81E-01	CHROMOSOME_II:7,840,969-7,840,982	14	srAwCGrCAyrCwy	rsGyrTGyCGsTyw
0 annotated groups 1 'de novo' group(s) 2486	115462	3.17E-01	CHROMOSOME_II:7,840,977-7,840,991	15	nTTCTTCTTCTTyTT	AArAAGAAGAAGAAn
0 annotated groups 1 'de novo' group(s) 7	115463	6.27E-01	CHROMOSOME_II:7,841,012-7,841,021	10	srTCGwCACw	sGTGsCGAyw
0 annotated groups 0 'de novo' group(s)	115464	5.91E-01	CHROMOSOME_II:7,841,050-7,841,063	14	TGArArTGTGwAAA	TTTsCACAyTyTCA
1 annotated group(s): 40117 (LXR-alpha) [7.63E-06] 1 'de novo' group(s) 368	115465	7.12E-01	CHROMOSOME_II:7,841,090-7,841,101	12	GTAAmCkAAyAm	kTrTTmGkTTAC
0 annotated groups 1 'de novo' group(s) 70	115466	8.18E-01	CHROMOSOME_II:7,841,100-7,841,114	15	AkwmGmTCGTTTGTk	mACAAACGAkCksmT
1 annotated group(s): 50106 (p53) [6.17E-05] 0 'de novo' group(s)	115467	2.30E-01	CHROMOSOME_II:7,841,121-7,841,132	12	TGAAATkGAATr	yATTCmATTTCA
0 annotated groups 0 'de novo' group(s)	115468	4.92E-02	CHROMOSOME_II:7,841,181-7,841,188	8	TCAAACAT	ATGTTTGA
1 annotated group(s): 40137 (NF-Y) [2.53E-06] 0 'de novo' group(s)	115469	8.48E-01	CHROMOSOME_II:7,841,194-7,841,209	16	GwCAGGTATTATTAGC	GCTAATAATACCTGsC
0 annotated groups 0 'de novo' group(s)	115470	6.40E-01	CHROMOSOME_II:7,841,216-7,841,227	12	CAGTAATTTTsG	CwAAAATTACTG
1 annotated group(s): 50014 (Bsap) [7.54E-05] 1 'de novo' group(s) 62	115471	5.78E-01	CHROMOSOME_II:7,841,225-7,841,238	14	TCGATCGTTTATTT	AAATAAACGATCGA
0 annotated groups 1 'de novo' group(s) 512	115472	7.08E-01	CHROMOSOME_II:7,841,253-7,841,269	17	rwkAGAsAAGATwAATG	CATTsATCTTwTCTmsy
0 annotated groups 0 'de novo' group(s)	115473	4.74E-01	CHROMOSOME_II:7,841,312-7,841,319	8	AAACGATC	GATCGTTT
0 annotated groups 0 'de novo' group(s)	115474	8.80E-01	CHROMOSOME_II:7,841,327-7,841,338	12	AAAyrATsArAA	TTyTwATyrTTT
0 annotated groups 0 'de novo' group(s)	115475	8.20E-02	CHROMOSOME_II:7,841,336-7,841,343	8	GAAwACAA	TTGTsTTC
0 annotated groups 0 'de novo' group(s)	115476	7.86E-01	CHROMOSOME_II:7,841,380-7,841,391	12	AAACrwkCrAsA	TwTyGmsyGTTT
0 annotated groups 0 'de novo' group(s)	115477	2.30E-01	CHROMOSOME_II:7,841,402-7,841,413	12	AATTACTGTTTT	AAAACAGTAATT
0 annotated groups 2 'de novo' group(s) 2966, 2103	115478	7.72E-01	CHROMOSOME_II:7,841,426-7,841,439	14	GGTAAACTAATAAA	TTTATTAGTTTACC
0 annotated groups 0 'de novo' group(s)	115479	5.24E-01	CHROMOSOME_II:7,841,447-7,841,456	10	CAGTwATTTT	AAAATsACTG
0 annotated groups 0 'de novo' group(s)	115480	3.16E-01	CHROMOSOME_II:7,841,465-7,841,472	8	TCTATACA	TGTATAGA
1 annotated group(s): 40188 (Sp3) [5.32E-06] 0 'de novo' group(s)	115481	4.60E-01	CHROMOSOME_II:7,841,476-7,841,490	15	ACArkAATTTTGGrr	yyCCAAAATTmyTGT
1 annotated group(s): 50041 (HFH-2) [9.31E-05] 0 'de novo' group(s)	115482	1.63E-01	CHROMOSOME_II:7,841,497-7,841,506	10	AATAAACkAk	mTmGTTTATT
0 annotated groups 0 'de novo' group(s)	115483	7.86E-01	CHROMOSOME_II:7,841,521-7,841,532	12	AwrATwmCTGTT	AACAGksATysT
0 annotated groups 0 'de novo' group(s)	115484	7.85E-02	CHROMOSOME_II:7,841,545-7,841,552	8	ACwCGACC	GGTCGsGT
0 annotated groups 0 'de novo' group(s)	115485	7.72E-01	CHROMOSOME_II:7,841,566-7,841,579	14	wCkATmAAyrmAmA	TkTkyrTTkATmGs
0 annotated groups 0 'de novo' group(s)	115486	4.73E-01	CHROMOSOME_II:7,841,575-7,841,586	12	rmAAAATAAACG	CGTTTATTTTky
0 annotated groups 3 'de novo' group(s) 902, 2430, 1694	115488	5.76E-01	CHROMOSOME_II:7,841,600-7,841,618	19	TGyTTGACrGCAAACAACA	TGTTGTTTGCyGTCAArCA
0 annotated groups 0 'de novo' group(s)	115487	6.32E-01	CHROMOSOME_II:7,841,610-7,841,621	12	CAAAmwAArCrr	yyGyTTskTTTG
1 annotated group(s): 40147 (NRSF) [8.10E-06] 0 'de novo' group(s)	115489	9.80E-02	CHROMOSOME_II:7,841,615-7,841,624	10	AAAACAGTAA	TTACTGTTTT
1 annotated group(s): 40147 (NRSF) [8.10E-06] 3 'de novo' group(s) 664, 1514, 2556	115490	6.42E-01	CHROMOSOME_II:7,841,628-7,841,643	16	GAkCrrswCACAmAwA	TsTkTGTGswyyGmTC
0 annotated groups 0 'de novo' group(s)	115491	3.16E-01	CHROMOSOME_II:7,841,656-7,841,665	10	TTkTTGkTCA	TGAmCAAmAA
0 annotated groups 2 'de novo' group(s) 2420, 1576	115494	9.17E-02	CHROMOSOME_II:7,841,685-7,841,701	17	CATTGTATTCAATTTCA	TGAAATTGAATACAATG
0 annotated groups 2 'de novo' group(s) 2420, 1576	115492	2.17E-01	CHROMOSOME_II:7,841,688-7,841,701	14	TGTATTCAATTTCA	TGAAATTGAATACA
1 annotated group(s): 50069 (Pax6) [9.23E-05] 1 'de novo' group(s) 1576	115493	2.17E-01	CHROMOSOME_II:7,841,689-7,841,702	14	GTATTCAATTTCAT	ATGAAATTGAATAC
1 annotated group(s): 50069 (Pax6) [9.23E-05] 3 'de novo' group(s) 1003, 3067, 1711	115495	5.13E-01	CHROMOSOME_II:7,841,694-7,841,728	35	CAATTTCATGTTTGATT...	CrrTrAAACAGCCGCAC...
0 annotated groups 1 'de novo' group(s) 1441	115496	5.50E-01	CHROMOSOME_II:7,841,723-7,841,734	12	TCGywACAAGCC	GGCTTGTsrCGA
3 annotated group(s): 40167 (PPAR-alpha) [6.84E-06] 40045 (COUP) [9.11E-06] 50065 (PPARgamma-RXRal) [5.54E-05] 0 'de novo' group(s)	115497	4.32E-01	CHROMOSOME_II:7,841,745-7,841,758	14	GCCCTTTCAACTTT	AAAGTTGAAAGGGC
0 annotated groups 0 'de novo' group(s)	115498	4.30E-01	CHROMOSOME_II:7,841,762-7,841,771	10	TCCwCkTCwT	AsGAmGsGGA
0 annotated groups 1 'de novo' group(s) 2950	115499	2.77E-01	CHROMOSOME_II:7,841,780-7,841,811	32	CwAwTTTTATTAGTTTA...	AAAAGTkAGAGAAGGTA...
1 annotated group(s): 50038 (Gfi) [8.18E-05] 4 'de novo' group(s) 16, 837, 1509, 2815	115500	2.12E-01	CHROMOSOME_II:7,841,811-7,841,827	17	TTTATGACGTGGmATCA	TGATkCCACGTCATAAA
1 annotated group(s): 50038 (Gfi) [8.18E-05] 2 'de novo' group(s) 2576, 1679	115501	6.62E-01	CHROMOSOME_II:7,841,821-7,841,836	16	AAAATTACTGTTTTTC	GAAAAACAGTAATTTT
0 annotated groups 2 'de novo' group(s) 2899, 1984	115503	5.13E-01	CHROMOSOME_II:7,841,862-7,841,881	20	CTnTAyTCGACCAGTTCTTC	GAAGAACTGGTCGArTAnAG
0 annotated groups 0 'de novo' group(s)	115502	3.62E-01	CHROMOSOME_II:7,841,865-7,841,872	8	yAyTCGAC	GTCGArTr
0 annotated groups 0 'de novo' group(s)	115504	6.40E-01	CHROMOSOME_II:7,841,878-7,841,891	14	TTTTynCTTCTTCT	AGAAGAAGnrAAAA
0 annotated groups 8 'de novo' group(s) 9, 172, 702, 844, 1546, 2773, 3018, 1607	115506	2.03E-01	CHROMOSOME_II:7,841,913-7,841,941	29	TTTTCCGCTAATAATAC...	ATTGTTGGTCAGGTATT...
0 annotated groups 2 'de novo' group(s) 702, 1546	115505	1.06E-01	CHROMOSOME_II:7,841,915-7,841,926	12	TTCCGCTAATAA	TTATTAGCGGAA
0 annotated groups 2 'de novo' group(s) 3159, 1960	115507	4.18E-01	CHROMOSOME_II:7,841,953-7,841,971	19	TTGGTCTTGTATAGAAGAn	nTCTTCTATACAAGACCAA
0 annotated groups 0 'de novo' group(s)	115508	3.11E-01	CHROMOSOME_II:7,841,966-7,841,978	13	GAAGACsACTTGA	TCAAGTwGTCTTC
0 annotated groups 0 'de novo' group(s)	115509	1.00E-08	CHROMOSOME_II:7,841,993-7,841,998	6	CCATTC	GAATGG
0 annotated groups 0 'de novo' group(s)	115510	8.20E-02	CHROMOSOME_II:7,842,011-7,842,018	8	TTACTkTT	AAmAGTAA
0 annotated groups 0 'de novo' group(s)	115511	5.02E-01	CHROMOSOME_II:7,842,027-7,842,040	14	wTTTCCTGTTnkwy	rsmnAACAGGAAAs
0 annotated groups 1 'de novo' group(s) 73	115512	6.26E-01	CHROMOSOME_II:7,842,034-7,842,053	20	GTykTkTTAGTTGCTwACyr	yrGTsAGCAACTAAmAmrAC
0 annotated groups 0 'de novo' group(s)	115513	8.19E-01	CHROMOSOME_II:7,842,047-7,842,069	23	CTArCTnAnAGATTATC...	AAAnAGGATAATCTnTn...
0 annotated groups 0 'de novo' group(s)	115514	7.95E-01	CHROMOSOME_II:7,842,078-7,842,087	10	AACGATCkAs	wTmGATCGTT
0 annotated groups 0 'de novo' group(s)	115515	8.22E-01	CHROMOSOME_II:7,842,083-7,842,092	10	TATACAAGAC	GTCTTGTATA
0 annotated groups 1 'de novo' group(s) 62	115516	5.38E-01	CHROMOSOME_II:7,842,110-7,842,120	11	TGTCGATCGTT	AACGATCGACA
1 annotated group(s): 50007 (Androgen) [4.69E-06] 0 'de novo' group(s)	115517	1.00E-08	CHROMOSOME_II:7,842,118-7,842,123	6	GTTGTT	AACAAC
0 annotated groups 0 'de novo' group(s)	115518	5.78E-01	CHROMOSOME_II:7,842,179-7,842,192	14	TGTCkATCsTyTwT	AsArAwGATmGACA
0 annotated groups 0 'de novo' group(s)	115519	8.27E-01	CHROMOSOME_II:7,842,199-7,842,212	14	AAAyGAwCrmyAmA	TkTrkyGsTCrTTT
0 annotated groups 3 'de novo' group(s) 596, 2884, 1878	115520	2.29E-01	CHROMOSOME_II:7,842,256-7,842,275	20	CCCyAAAATTACTGTTTTTC	GAAAAACAGTAATTTTrGGG
0 annotated groups 5 'de novo' group(s) 107, 818, 2671, 1705, 2263	115521	1.01E-01	CHROMOSOME_II:7,842,279-7,842,306	28	AAAAATAAACGATCGAC...	TrTTTGTGTGTGTCGAT...
0 annotated groups 0 'de novo' group(s)	115522	1.00E-08	CHROMOSOME_II:7,842,306-7,842,311	6	ACAGGA	TCCTGT