Region for Gene F57B9.7a

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 31 out of 31 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) 201, 2914	82785	4.66E-02	CHROMOSOME_III:6,928,848-6,928,865	18	CATTACACTCATTTTCAC	GTGAAAATGAGTGTAATG
0 annotated groups 1 'de novo' group(s) 76	82784	8.80E-01	CHROMOSOME_III:6,928,865-6,928,876	12	CGCGGAnrmAAC	GTTkynTCCGCG
0 annotated groups 13 'de novo' group(s) 38, 76, 108, 561, 657, 2414, 2453, 2475, 2658, 3161, 1614, 1675, 1799	82782	1.67E-01	CHROMOSOME_III:6,928,871-6,928,931	61	wCnCTCACACATATTGA...	nCCGCGGGTTGTGTCCG...
0 annotated groups 0 'de novo' group(s)	82781	1.40E-01	CHROMOSOME_III:6,928,933-6,928,940	8	nCTCACTC	GAGTGAGn
2 annotated group(s): 50014 (Bsap) [2.87E-06] 40154 (Pax-5) [5.64E-06] 1 'de novo' group(s) 3164	82780	5.91E-01	CHROMOSOME_III:6,928,941-6,928,959	19	TCTCsCTCATTTsCCTmnn	nnkAGGwAAATGAGwGAGA
2 annotated group(s): 50072 (RORalfa-2) [1.49E-05] 50071 (RORalfa-1) [5.76E-05] 0 'de novo' group(s)	82779	4.74E-01	CHROMOSOME_III:6,929,097-6,929,108	12	ATTGACATAAAT	ATTTATGTCAAT
0 annotated groups 0 'de novo' group(s)	82778	8.56E-01	CHROMOSOME_III:6,929,119-6,929,128	10	TCCGCGCGGA	TCCGCGCGGA
3 annotated group(s): 40212 (ZEB_(1124_AA)) [1.01E-06] 40015 (AP-4) [3.50E-06] 40212 (ZEB_(1124_AA)) [8.85E-06] 2 'de novo' group(s) 18, 2247	82777	9.90E-02	CHROMOSOME_III:6,929,166-6,929,179	14	AACACCTGTTGACA	TGTCAACAGGTGTT
3 annotated group(s): 40016 (AR) [2.39E-06] 40115 (Lmo2) [5.06E-06] 50091 (Tal1beta-E47S) [2.56E-05] 3 'de novo' group(s) 624, 3039, 1817	82776	4.86E-02	CHROMOSOME_III:6,929,188-6,929,201	14	AGAACACCATCTGC	GCAGATGGTGTTCT
1 annotated group(s): 40016 (AR) [2.39E-06] 0 'de novo' group(s)	82775	6.73E-01	CHROMOSOME_III:6,929,197-6,929,210	14	rAATCkCGAAGAAC	GTTCTTCGmGATTy
0 annotated groups 3 'de novo' group(s) 11, 182, 1364	82774	9.57E-01	CHROMOSOME_III:6,929,231-6,929,250	20	TTCTnCmGCGGGTTGTGTCC	GGACACAACCCGCkGnAGAA
0 annotated groups 1 'de novo' group(s) 996	82773	9.64E-01	CHROMOSOME_III:6,929,253-6,929,266	14	GAATCCGCGCGGAC	GTCCGCGCGGATTC
0 annotated groups 0 'de novo' group(s)	82772	2.30E-01	CHROMOSOME_III:6,929,260-6,929,271	12	AATGAGTGTAAT	ATTACACTCATT
0 annotated groups 5 'de novo' group(s) 167, 1523, 2711, 3064, 2056	82771	3.58E-01	CHROMOSOME_III:6,929,270-6,929,298	29	GAGCAATTTAGGCAAAT...	yyCTTCTCGCTCATTTG...
0 annotated groups 1 'de novo' group(s) 30	82770	7.88E-01	CHROMOSOME_III:6,929,300-6,929,310	11	TCCGCGCGGAC	GTCCGCGCGGA
0 annotated groups 0 'de novo' group(s)	82769	1.40E-01	CHROMOSOME_III:6,929,366-6,929,373	8	ATGAGTGT	ACACTCAT
0 annotated groups 0 'de novo' group(s)	82768	4.24E-01	CHROMOSOME_III:6,929,427-6,929,439	13	CTTCGAGATTTAT	ATAAATCTCGAAG
0 annotated groups 1 'de novo' group(s) 7	82767	3.16E-01	CHROMOSOME_III:6,929,457-6,929,466	10	GACGACwGAG	CTCsGTCGTC
0 annotated groups 0 'de novo' group(s)	82766	6.76E-01	CHROMOSOME_III:6,929,464-6,929,477	14	TCnCTCACACwTAT	ATAsGTGTGAGnGA
0 annotated groups 0 'de novo' group(s)	82765	8.80E-01	CHROMOSOME_III:6,929,498-6,929,509	12	GAATCCGCGCGG	CCGCGCGGATTC
1 annotated group(s): 40084 (FXR) [7.60E-06] 0 'de novo' group(s)	82764	6.10E-01	CHROMOSOME_III:6,929,577-6,929,586	10	ATTACACTCA	TGAGTGTAAT
0 annotated groups 0 'de novo' group(s)	82763	9.57E-01	CHROMOSOME_III:6,929,665-6,929,682	18	AAGAAAnATTACACTCAT	ATGAGTGTAATnTTTCTT
0 annotated groups 0 'de novo' group(s)	82762	1.00E-08	CHROMOSOME_III:6,929,697-6,929,704	8	TCTCGAAG	CTTCGAGA
0 annotated groups 0 'de novo' group(s)	82761	2.10E-01	CHROMOSOME_III:6,929,707-6,929,716	10	rrGAGTGACG	CGTCACTCyy
0 annotated groups 0 'de novo' group(s)	82760	7.12E-01	CHROMOSOME_III:6,929,725-6,929,736	12	CCGCGCGGATTC	GAATCCGCGCGG
1 annotated group(s): 50101 (c-REL) [5.63E-05] 2 'de novo' group(s) 5, 2925	82759	6.45E-01	CHROMOSOME_III:6,929,735-6,929,751	17	GAAACCGCCCCAAAACC	GGTTTTGGGGCGGTTTC
0 annotated groups 0 'de novo' group(s)	82758	5.55E-01	CHROMOSOME_III:6,929,812-6,929,827	16	wTTGAmATAAATnTnG	CnAnATTTATkTCAAs
0 annotated groups 0 'de novo' group(s)	82757	6.10E-01	CHROMOSOME_III:6,929,852-6,929,861	10	GACATAAATC	GATTTATGTC
0 annotated groups 0 'de novo' group(s)	82756	2.06E-01	CHROMOSOME_III:6,929,911-6,929,920	10	kTATnTCAAT	ATTGAnATAm
0 annotated groups 0 'de novo' group(s)	82755	4.98E-01	CHROMOSOME_III:6,929,990-6,930,003	14	nnAAATyTCGAArG	CyTTCGArATTTnn
0 annotated groups 0 'de novo' group(s)	82754	1.00E-08	CHROMOSOME_III:6,930,030-6,930,035	6	AGTGCG	CGCACT