Region for Gene AH6.5

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 32 out of 32 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)	273	4.39E-01	CHROMOSOME_II:9,522,601-9,522,614	14	CTCTyyTnwCTTTG	CAAAGsnArrAGAG
0 annotated groups 0 'de novo' group(s)	274	6.73E-01	CHROMOSOME_II:9,522,629-9,522,634	6	AAGTAG	CTACTT
0 annotated groups 0 'de novo' group(s)	275	6.40E-01	CHROMOSOME_II:9,522,654-9,522,665	12	TTTTnAArCAGA	TCTGyTTnAAAA
3 annotated group(s): 50025 (E4BP4) [2.02E-05] 50014 (Bsap) [4.15E-05] 50043 (HLF) [5.24E-05] 1 'de novo' group(s) 1876	276	6.66E-01	CHROMOSOME_II:9,522,675-9,522,691	17	TnnATTACTTCAyTTTT	AAAArTGAAGTAATnnA
0 annotated groups 0 'de novo' group(s)	277	7.91E-01	CHROMOSOME_II:9,522,769-9,522,788	20	nwTTACTTCwCTTTTnnTTn	nAAnnAAAAGsGAAGTAAsn
0 annotated groups 0 'de novo' group(s)	278	1.40E-01	CHROMOSOME_II:9,522,792-9,522,799	8	AAGAATTA	TAATTCTT
0 annotated groups 0 'de novo' group(s)	279	9.08E-01	CHROMOSOME_II:9,522,796-9,522,805	10	ATAACATATC	GATATGTTAT
0 annotated groups 0 'de novo' group(s)	280	1.00E-08	CHROMOSOME_II:9,522,848-9,522,853	6	TGTTTC	GAAACA
0 annotated groups 0 'de novo' group(s)	281	5.50E-01	CHROMOSOME_II:9,522,859-9,522,870	12	TACkrTwTACGT	ACGTAsAymGTA
0 annotated groups 1 'de novo' group(s) 94	282	5.38E-01	CHROMOSOME_II:9,522,867-9,522,877	11	rnGTACTGTAn	nTACAGTACny
0 annotated groups 0 'de novo' group(s)	283	5.15E-01	CHROMOSOME_II:9,523,074-9,523,083	10	TTwTmAGnTT	AAnCTkAsAA
1 annotated group(s): 40154 (Pax-5) [7.20E-06] 0 'de novo' group(s)	284	9.23E-01	CHROMOSOME_II:9,523,145-9,523,156	12	CAGTCAAGATCA	TGATCTTGACTG
1 annotated group(s): 40164 (POU2F1) [5.60E-06] 0 'de novo' group(s)	285	8.40E-02	CHROMOSOME_II:9,523,165-9,523,172	8	TTwATGCA	TGCATsAA
0 annotated groups 0 'de novo' group(s)	286	5.14E-01	CHROMOSOME_II:9,523,269-9,523,278	10	GTAATTCGyn	nrCGAATTAC
0 annotated groups 0 'de novo' group(s)	287	3.16E-01	CHROMOSOME_II:9,523,339-9,523,348	10	TTTmGCTGmA	TkCAGCkAAA
0 annotated groups 0 'de novo' group(s)	288	9.23E-01	CHROMOSOME_II:9,523,399-9,523,410	12	TGATCTTGACTG	CAGTCAAGATCA
0 annotated groups 0 'de novo' group(s)	289	8.20E-02	CHROMOSOME_II:9,523,438-9,523,445	8	ATTCnTTG	CAAnGAAT
0 annotated groups 0 'de novo' group(s)	290	2.67E-01	CHROMOSOME_II:9,523,459-9,523,475	17	CAAArAATGAAGTAATA	TATTACTTCATTyTTTG
0 annotated groups 0 'de novo' group(s)	291	5.76E-01	CHROMOSOME_II:9,523,476-9,523,490	15	AwTTwCwTyATTTTT	AAAAATrAsGsAAsT
0 annotated groups 2 'de novo' group(s) 94, 596	292	6.27E-01	CHROMOSOME_II:9,523,583-9,523,593	11	TACAGTAmyyn	nrrkTACTGTA
0 annotated groups 0 'de novo' group(s)	293	3.12E-01	CHROMOSOME_II:9,523,611-9,523,620	10	AAGGmGCrTA	TAyGCkCCTT
0 annotated groups 4 'de novo' group(s) 6, 675, 2773, 1570	295	6.74E-01	CHROMOSOME_II:9,523,638-9,523,661	24	nGTCTCGCnACGnnTAC...	GrnTACkGTAnnCGTnG...
0 annotated groups 1 'de novo' group(s) 2773	294	9.31E-01	CHROMOSOME_II:9,523,643-9,523,656	14	CnCCACGAATACCG	CGGTATTCGTGGnG
1 annotated group(s): 40138 (Nkx2-1) [4.55E-06] 1 'de novo' group(s) 363	296	8.74E-01	CHROMOSOME_II:9,523,666-9,523,673	8	GGTAAATC	GATTTACC
0 annotated groups 3 'de novo' group(s) 38, 591, 2007	297	9.68E-01	CHROMOSOME_II:9,523,693-9,523,704	12	GACCGCCGGCGC	GCGCCGGCGGTC
0 annotated groups 0 'de novo' group(s)	298	1.92E-01	CHROMOSOME_II:9,523,823-9,523,834	12	TCTGCyTnAAAA	TTTTnArGCAGA
0 annotated groups 0 'de novo' group(s)	299	7.98E-01	CHROMOSOME_II:9,523,923-9,523,940	18	GTwCATTAATTArnCnsA	TwnGnyTAATTAATGsAC
0 annotated groups 0 'de novo' group(s)	300	1.00E-08	CHROMOSOME_II:9,523,964-9,523,969	6	CAGCTA	TAGCTG
0 annotated groups 0 'de novo' group(s)	301	5.49E-01	CHROMOSOME_II:9,524,011-9,524,022	12	CnTCCTGCATkA	TmATGCAGGAnG
0 annotated groups 0 'de novo' group(s)	302	1.00E-08	CHROMOSOME_II:9,524,021-9,524,026	6	GAAACA	TGTTTC
0 annotated groups 0 'de novo' group(s)	303	6.95E-01	CHROMOSOME_II:9,524,033-9,524,044	12	wTTTkACTGnGT	ACnCAGTmAAAs
0 annotated groups 0 'de novo' group(s)	304	2.99E-01	CHROMOSOME_II:9,524,082-9,524,093	12	TTTTnArrCAGA	TCTGyyTnAAAA