Region for Gene B0035.1b

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 61 out of 61 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)	897	8.52E-01	CHROMOSOME_IV:11,309,506-11,309,515	10	CGAAGGGAAC	GTTCCCTTCG
0 annotated groups 0 'de novo' group(s)	898	7.72E-01	CHROMOSOME_IV:11,309,526-11,309,539	14	CATTTTTATGCnnw	snnGCATAAAAATG
1 annotated group(s): 50057 (MZF_5-13) [9.29E-05] 1 'de novo' group(s) 504	899	9.97E-01	CHROMOSOME_IV:11,309,548-11,309,561	14	AAAATTGCGCGGCA	TGCCGCGCAATTTT
0 annotated groups 0 'de novo' group(s)	900	8.06E-01	CHROMOSOME_IV:11,309,584-11,309,597	14	AAAGAAGAAAAGAA	TTCTTTTCTTCTTT
1 annotated group(s): 50014 (Bsap) [1.00E-05] 0 'de novo' group(s)	901	5.77E-01	CHROMOSOME_IV:11,309,607-11,309,616	10	GyAAGnyGAC	GTCrnCTTrC
0 annotated groups 0 'de novo' group(s)	902	2.13E-01	CHROMOSOME_IV:11,309,663-11,309,674	12	TAwTTnATAAAT	ATTTATnAAsTA
0 annotated groups 0 'de novo' group(s)	903	7.51E-01	CHROMOSOME_IV:11,309,680-11,309,702	23	GTAAATArCTwTTTAAT...	AnnTnnATTAAAsAGyT...
0 annotated groups 0 'de novo' group(s)	904	4.74E-01	CHROMOSOME_IV:11,309,718-11,309,723	6	ATAATA	TATTAT
0 annotated groups 2 'de novo' group(s) 3251, 2360	905	4.56E-01	CHROMOSOME_IV:11,309,792-11,309,806	15	GGnAAATwGCTwTTT	AAAsAGCsATTTnCC
1 annotated group(s): 40201 (TEF) [5.06E-06] 0 'de novo' group(s)	906	3.63E-01	CHROMOSOME_IV:11,309,810-11,309,821	12	AATmTwTAAAnn	nnTTTAsAkATT
0 annotated groups 0 'de novo' group(s)	907	8.17E-01	CHROMOSOME_IV:11,309,827-11,309,840	14	AAAATAATTAAAAT	ATTTTAATTATTTT
0 annotated groups 0 'de novo' group(s)	909	7.49E-01	CHROMOSOME_IV:11,309,927-11,309,943	17	AACTTTATnnnAnAnwT	AsnTnTnnnATAAAGTT
0 annotated groups 0 'de novo' group(s)	908	3.16E-01	CHROMOSOME_IV:11,309,934-11,309,943	10	TTGAAAkGTT	AACmTTTCAA
0 annotated groups 0 'de novo' group(s)	910	9.53E-01	CHROMOSOME_IV:11,309,944-11,309,955	12	CGCAATGGACGA	TCGTCCATTGCG
0 annotated groups 0 'de novo' group(s)	911	9.82E-01	CHROMOSOME_IV:11,309,956-11,309,965	10	TAGTAAATCG	CGATTTACTA
0 annotated groups 0 'de novo' group(s)	912	2.83E-01	CHROMOSOME_IV:11,309,970-11,309,981	12	CGCACTTTTCAA	TTGAAAAGTGCG
0 annotated groups 0 'de novo' group(s)	913	8.20E-01	CHROMOSOME_IV:11,310,017-11,310,026	10	AATATTAACA	TGTTAATATT
0 annotated groups 0 'de novo' group(s)	914	8.57E-01	CHROMOSOME_IV:11,310,022-11,310,035	14	GAACnTTTTAAAmn	nkTTTAAAAnGTTC
0 annotated groups 0 'de novo' group(s)	915	9.94E-01	CHROMOSOME_IV:11,310,091-11,310,104	14	GTTTCAAAGTTnTT	AAnAACTTTGAAAC
0 annotated groups 0 'de novo' group(s)	916	5.91E-01	CHROMOSOME_IV:11,310,101-11,310,110	10	TGTTAATATT	AATATTAACA
0 annotated groups 0 'de novo' group(s)	917	9.80E-02	CHROMOSOME_IV:11,310,127-11,310,136	10	mACATTTCAA	TTGAAATGTk
0 annotated groups 0 'de novo' group(s)	918	7.52E-01	CHROMOSOME_IV:11,310,158-11,310,171	14	AAwTTrTTAnAATA	TATTnTAAyAAsTT
0 annotated groups 0 'de novo' group(s)	919	1.91E-01	CHROMOSOME_IV:11,310,188-11,310,197	10	AAyTTTGTAA	TTACAAArTT
0 annotated groups 0 'de novo' group(s)	920	2.00E-01	CHROMOSOME_IV:11,310,195-11,310,200	6	wAAGTT	AACTTs
0 annotated groups 0 'de novo' group(s)	921	4.74E-01	CHROMOSOME_IV:11,310,213-11,310,218	6	TTGCAA	TTGCAA
0 annotated groups 0 'de novo' group(s)	922	2.66E-01	CHROMOSOME_IV:11,310,240-11,310,251	12	CTGAAATrTGCG	CGCAyATTTCAG
0 annotated groups 0 'de novo' group(s)	923	7.77E-01	CHROMOSOME_IV:11,310,252-11,310,267	16	TnnTTAnAwAGTTATn	nATAACTsTnTAAnnA
0 annotated groups 0 'de novo' group(s)	924	2.81E-01	CHROMOSOME_IV:11,310,261-11,310,272	12	AsTTATGTGyGT	ACrCACATAAwT
0 annotated groups 0 'de novo' group(s)	925	5.02E-01	CHROMOSOME_IV:11,310,281-11,310,290	10	AACAACTTnn	nnAAGTTGTT
0 annotated groups 0 'de novo' group(s)	926	9.04E-02	CHROMOSOME_IV:11,310,304-11,310,311	8	TTTTAAAG	CTTTAAAA
0 annotated groups 0 'de novo' group(s)	927	1.45E-01	CHROMOSOME_IV:11,310,326-11,310,335	10	TAyTnTTATA	TATAAnArTA
0 annotated groups 0 'de novo' group(s)	928	1.94E-01	CHROMOSOME_IV:11,310,333-11,310,340	8	AAAGAATA	TATTCTTT
0 annotated groups 0 'de novo' group(s)	929	7.73E-01	CHROMOSOME_IV:11,310,357-11,310,378	22	nATnATwATAAnAkTAA...	nAnAGTTAmTnTTATsA...
1 annotated group(s): 50072 (RORalfa-2) [9.78E-05] 1 'de novo' group(s) 23	930	5.00E-01	CHROMOSOME_IV:11,310,383-11,310,401	19	GTTACTCAnATAnAnnTTn	nAAnnTnTATnTGAGTAAC
1 annotated group(s): 30009 (DAF-19) [7.37E-05] 0 'de novo' group(s)	931	4.59E-01	CHROMOSOME_IV:11,310,415-11,310,427	13	srCATTTTTATGm	kCATAAAAATGyw
2 annotated group(s): 50025 (E4BP4) [2.88E-05] 30009 (DAF-19) [7.37E-05] 0 'de novo' group(s)	932	7.44E-01	CHROMOSOME_IV:11,310,424-11,310,437	14	AwGwCrACTTnCnw	snGnAAGTyGsCsT
0 annotated groups 0 'de novo' group(s)	933	4.74E-01	CHROMOSOME_IV:11,310,446-11,310,451	6	TAAACA	TGTTTA
0 annotated groups 0 'de novo' group(s)	934	9.04E-02	CHROMOSOME_IV:11,310,451-11,310,458	8	AATAAATT	AATTTATT
0 annotated groups 0 'de novo' group(s)	935	9.28E-01	CHROMOSOME_IV:11,310,456-11,310,465	10	AGTCGACTTA	TAAGTCGACT
0 annotated groups 0 'de novo' group(s)	936	1.00E-08	CHROMOSOME_IV:11,310,474-11,310,479	6	ATTTAT	ATAAAT
0 annotated groups 0 'de novo' group(s)	937	7.44E-01	CHROMOSOME_IV:11,310,491-11,310,504	14	TTATAAAGTTATnn	nnATAACTTTATAA
0 annotated groups 0 'de novo' group(s)	938	9.08E-01	CHROMOSOME_IV:11,310,508-11,310,517	10	CTATAAGAAT	ATTCTTATAG
0 annotated groups 0 'de novo' group(s)	939	3.30E-01	CHROMOSOME_IV:11,310,522-11,310,529	8	AyGACTTT	AAAGTCrT
0 annotated groups 0 'de novo' group(s)	940	9.04E-02	CHROMOSOME_IV:11,310,526-11,310,533	8	CTTTAAAA	TTTTAAAG
0 annotated groups 0 'de novo' group(s)	941	7.85E-01	CHROMOSOME_IV:11,310,536-11,310,547	12	TATTCAAACGAA	TTCGTTTGAATA
0 annotated groups 0 'de novo' group(s)	942	4.74E-01	CHROMOSOME_IV:11,310,562-11,310,567	6	TTGCAA	TTGCAA
0 annotated groups 0 'de novo' group(s)	943	8.48E-01	CHROMOSOME_IV:11,310,571-11,310,576	6	TTAAGA	TCTTAA
0 annotated groups 0 'de novo' group(s)	944	7.43E-01	CHROMOSOME_IV:11,310,591-11,310,600	10	ACAGTCAGTT	AACTGACTGT
2 annotated group(s): 40008 (AML1) [5.83E-06] 40008 (AML1) [7.86E-06] 2 'de novo' group(s) 39, 1301	945	8.63E-01	CHROMOSOME_IV:11,310,618-11,310,631	14	TGGTATACGTTTCA	TGAAACGTATACCA
0 annotated groups 0 'de novo' group(s)	946	2.92E-01	CHROMOSOME_IV:11,310,665-11,310,683	19	TATTnTAATAAATTTnAAA	TTTnAAATTTATTAnAATA
0 annotated groups 0 'de novo' group(s)	947	8.63E-02	CHROMOSOME_IV:11,310,681-11,310,690	10	AAAAATGTsT	AwACATTTTT
0 annotated groups 0 'de novo' group(s)	948	9.96E-01	CHROMOSOME_IV:11,310,728-11,310,741	14	GGAAACGTTTAAAA	TTTTAAACGTTTCC
0 annotated groups 2 'de novo' group(s) 38, 770	949	5.39E-01	CHROMOSOME_IV:11,310,760-11,310,774	15	AAAnnTGCGCGGCrs	wyGCCGCGCAnnTTT
0 annotated groups 0 'de novo' group(s)	950	9.48E-01	CHROMOSOME_IV:11,310,809-11,310,818	10	TGyGCGGCAC	GTGCCGCrCA
0 annotated groups 0 'de novo' group(s)	951	3.80E-01	CHROMOSOME_IV:11,310,822-11,310,833	12	rCAAAATTGAAT	ATTCAATTTTGy
0 annotated groups 0 'de novo' group(s)	952	8.75E-01	CHROMOSOME_IV:11,310,850-11,310,859	10	GTTCCnTTCG	CGAAnGGAAC
0 annotated groups 0 'de novo' group(s)	953	3.11E-01	CHROMOSOME_IV:11,310,863-11,310,874	12	AAATAwwTTAAA	TTTAAssTATTT
1 annotated group(s): 30006 (CEH-10) [1.65E-05] 0 'de novo' group(s)	954	9.61E-01	CHROMOSOME_IV:11,310,902-11,310,915	14	GTTTTAAAATTTGT	ACAAATTTTAAAAC
1 annotated group(s): 30006 (CEH-10) [1.65E-05] 0 'de novo' group(s)	955	9.08E-01	CHROMOSOME_IV:11,310,913-11,310,922	10	AGTTGACTTA	TAAGTCAACT
0 annotated groups 0 'de novo' group(s)	956	6.85E-01	CHROMOSOME_IV:11,310,920-11,310,936	17	TTATTCTTTTCTTCnnn	nnnGAAGAAAAGAATAA
0 annotated groups 0 'de novo' group(s)	957	1.07E-01	CHROMOSOME_IV:11,310,944-11,310,951	8	TATAAATA	TATTTATA