Region for Gene B0041.2c

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 49 out of 49 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)	1159	1.40E-01	CHROMOSOME_I:4,655,084-4,655,091	8	GCCAACCG	CGGTTGGC
0 annotated groups 2 'de novo' group(s) 6, 79	1160	6.45E-01	CHROMOSOME_I:4,655,155-4,655,167	13	CAACCGTCCCCGT	ACGGGGACGGTTG
0 annotated groups 0 'de novo' group(s)	1161	6.10E-01	CHROMOSOME_I:4,655,197-4,655,206	10	CCGTCCCCGT	ACGGGGACGG
1 annotated group(s): 50014 (Bsap) [8.62E-05] 8 'de novo' group(s) 14, 89, 151, 577, 978, 1495, 2600, 3056	1162	4.70E-01	CHROMOSOME_I:4,655,346-4,655,372	27	TCAGCCAAACGAGGCGG...	ATACCCGGATCCGCCTC...
0 annotated groups 7 'de novo' group(s) 53, 61, 139, 296, 466, 787, 1581	1163	4.16E-02	CHROMOSOME_I:4,655,365-4,655,396	32	CCGGGTATGAACGGGGA...	GGTCCTTGCCAACCGTC...
1 annotated group(s): 40003 (AhR) [5.05E-06] 7 'de novo' group(s) 17, 34, 61, 118, 705, 907, 1994	1164	8.67E-02	CHROMOSOME_I:4,655,391-4,655,438	48	ACCTGGTGGCCGTGGAG...	CnTCCTCCGCCACCATT...
0 annotated groups 5 'de novo' group(s) 7, 25, 315, 1716, 1857	1167	7.66E-01	CHROMOSOME_I:4,655,437-4,655,464	28	srAsGACCTGGTGGCCG...	GTGnTCCTCCACGGCCA...
0 annotated groups 1 'de novo' group(s) 229	1168	5.13E-01	CHROMOSOME_I:4,655,486-4,655,502	17	ATCAnCATCATGGTrAG	CTyACCATGATGnTGAT
1 annotated group(s): 30001 (11997337-HSAS) [4.94E-05] 1 'de novo' group(s) 54	1169	9.10E-01	CHROMOSOME_I:4,655,517-4,655,530	14	TkGGGwGACGCnGA	TCnGCGTCsCCCmA
0 annotated groups 0 'de novo' group(s)	1170	1.00E-08	CHROMOSOME_I:4,655,573-4,655,578	6	TGCTGC	GCAGCA
0 annotated groups 0 'de novo' group(s)	1171	4.34E-01	CHROMOSOME_I:4,655,720-4,655,734	15	AGGTGGmATsAwTCG	CGAsTwATkCCACCT
0 annotated groups 3 'de novo' group(s) 51, 593, 2161	1172	1.98E-01	CHROMOSOME_I:4,655,728-4,655,748	21	TGAATCGwATGATGCCA...	CnGGTGGCATCATsCGA...
0 annotated groups 2 'de novo' group(s) 60, 127	1173	4.26E-01	CHROMOSOME_I:4,655,753-4,655,767	15	nCGmCCACAACAAsA	TwTTGTTGTGGkCGn
1 annotated group(s): 50069 (Pax6) [5.14E-05] 0 'de novo' group(s)	1174	3.72E-01	CHROMOSOME_I:4,655,769-4,655,782	14	CAATAyATGCCTCC	GGAGGCATrTATTG
4 annotated group(s): 40174 (Roaz) [2.79E-06] 40035 (CACCC-binding_factor) [5.08E-06] 40037 (CBF(2)) [8.86E-06] ... 1 'de novo' group(s) 33	1175	8.39E-01	CHROMOSOME_I:4,655,783-4,655,817	35	nnnTCCnymnnnnCCAC...	CnGGCATTCCACCCATT...
0 annotated groups 0 'de novo' group(s)	1176	8.46E-01	CHROMOSOME_I:4,655,816-4,655,829	14	TGATGTGATsswyC	GrswwATCACATCA
0 annotated groups 2 'de novo' group(s) 75, 1066	1177	8.93E-02	CHROMOSOME_I:4,655,825-4,655,854	30	GGATnTnAAyATGCGAA...	GACATACCATCCATTCG...
0 annotated groups 1 'de novo' group(s) 601	1179	7.52E-01	CHROMOSOME_I:4,655,859-4,655,875	17	GCATCGACACCAwCnnn	nnnGsTGGTGTCGATGC
1 annotated group(s): 40167 (PPAR-alpha) [3.20E-06] 5 'de novo' group(s) 68, 290, 1276, 3218, 2221	1180	9.53E-01	CHROMOSOME_I:4,655,886-4,655,929	44	CArTnnGGnGATATGGG...	nGmTnnnnTnGTTGTGG...
0 annotated groups 0 'de novo' group(s)	1181	2.58E-01	CHROMOSOME_I:4,655,927-4,655,941	15	TCAACCkGCTCCATT	AATGGAGCmGGTTGA
0 annotated groups 0 'de novo' group(s)	1182	7.72E-01	CHROMOSOME_I:4,655,934-4,655,947	14	TCCCCGTTCATACC	GGTATGAACGGGGA
0 annotated groups 1 'de novo' group(s) 1857	1183	5.06E-01	CHROMOSOME_I:4,655,943-4,655,961	19	GyrCCnCCACCwCAACAnG	CnTGTTGsGGTGGnGGyrC
1 annotated group(s): 50007 (Androgen) [9.91E-05] 0 'de novo' group(s)	1184	9.68E-02	CHROMOSOME_I:4,655,960-4,655,975	16	AGACGATCTCTATGAT	ATCATAGAGATCGTCT
0 annotated groups 4 'de novo' group(s) 96, 1315, 3125, 2146	1185	8.47E-01	CHROMOSOME_I:4,655,981-4,655,999	19	nnnnwATGGTGGyGGwGsw	swCsCCrCCACCATsnnnn
0 annotated groups 2 'de novo' group(s) 239, 2739	1186	5.38E-01	CHROMOSOME_I:4,655,996-4,656,017	22	ACCTGGTGGCCGTGGAG...	TGnTCCTCCACGGCCAC...
0 annotated groups 2 'de novo' group(s) 239, 705	1187	7.72E-01	CHROMOSOME_I:4,656,010-4,656,023	14	GGTGGCATCATnCG	CGnATGATGCCACC
1 annotated group(s): 50091 (Tal1beta-E47S) [4.43E-05] 0 'de novo' group(s)	1188	4.15E-01	CHROMOSOME_I:4,656,026-4,656,045	20	wCAnATGCCACCnTATGGnC	GnCCATAnGGTGGCATnTGs
0 annotated groups 0 'de novo' group(s)	1189	4.58E-01	CHROMOSOME_I:4,656,063-4,656,079	17	AAnCAATACGGGAATAG	CTATTCCCGTATTGnTT
2 annotated group(s): 30004 (15492775-EARLY-2) [1.66E-05] 50074 (RXR-VDR) [5.05E-05] 1 'de novo' group(s) 130	1190	7.48E-01	CHROMOSOME_I:4,656,091-4,656,109	19	nnmAnGGTGGnTATGGwGG	CCsCCATAnCCACCnTknn
2 annotated group(s): 40147 (NRSF) [1.27E-07] 50048 (Hen-1) [3.85E-05] 0 'de novo' group(s)	1191	9.17E-02	CHROMOSOME_I:4,656,119-4,656,128	10	GAGGCArCAG	CTGyTGCCTC
2 annotated group(s): 40147 (NRSF) [1.27E-07] 50048 (Hen-1) [3.85E-05] 0 'de novo' group(s)	1192	5.18E-01	CHROMOSOME_I:4,656,126-4,656,142	17	mAnCAnCAACAGCCACC	GGTGGCTGTTGnTGnTk
0 annotated groups 0 'de novo' group(s)	1193	1.61E-01	CHROMOSOME_I:4,656,154-4,656,172	19	ACATGCCnCCAATGATGGT	ACCATCATTGGnGGCATGT
1 annotated group(s): 40197 (Tal-1) [5.30E-06] 4 'de novo' group(s) 18, 131, 1154, 1985	1194	9.52E-01	CHROMOSOME_I:4,656,169-4,656,194	26	nnnnwCnnCnwCnTCmG...	rAATGGTGGCkGAnGsn...
0 annotated groups 0 'de novo' group(s)	1195	4.39E-01	CHROMOSOME_I:4,656,195-4,656,211	17	nAnGGTGGAAATCAGmm	kkCTGATTTCCACCnTn
0 annotated groups 0 'de novo' group(s)	1196	4.95E-01	CHROMOSOME_I:4,656,219-4,656,232	14	CAnCAACArCmACC	GGTkGyTGTTGnTG
0 annotated groups 0 'de novo' group(s)	1197	1.35E-01	CHROMOSOME_I:4,656,240-4,656,260	21	GCwCCrTCrCCATTCTC...	CATTGAGAATGGyGAyG...
0 annotated groups 0 'de novo' group(s)	1198	4.30E-01	CHROMOSOME_I:4,656,261-4,656,277	17	GGTGGwGGTGGTGGmnn	nnkCCACCACCsCCACC
0 annotated groups 2 'de novo' group(s) 61, 144	1199	8.32E-01	CHROMOSOME_I:4,656,273-4,656,294	22	AGAAGGnCACGArGArG...	rAAGTCyTCyTCGTGnC...
2 annotated group(s): 40197 (Tal-1) [5.30E-06] 50007 (Androgen) [4.04E-05] 5 'de novo' group(s) 18, 36, 620, 3235, 1985	1200	6.43E-01	CHROMOSOME_I:4,656,300-4,656,317	18	TGGCAAGGACCwGGTGGn	nCCACCsGGTCCTTGCCA
1 annotated group(s): 40197 (Tal-1) [5.30E-06] 0 'de novo' group(s)	1201	2.07E-01	CHROMOSOME_I:4,656,312-4,656,325	14	GGTGGAAATCAGAA	TTCTGATTTCCACC
0 annotated groups 0 'de novo' group(s)	1202	1.00E-08	CHROMOSOME_I:4,656,326-4,656,331	6	TGGAGG	CCTCCA
0 annotated groups 0 'de novo' group(s)	1203	9.08E-01	CHROMOSOME_I:4,656,330-4,656,343	14	GCATksGGwGATkC	GmATCsCCwmATGC
0 annotated groups 1 'de novo' group(s) 68	1204	1.00E-08	CHROMOSOME_I:4,656,367-4,656,384	18	CAATGTGGACTGATGAGA	TCTCATCAGTCCACATTG
0 annotated groups 1 'de novo' group(s) 1626	1205	6.58E-02	CHROMOSOME_I:4,656,377-4,656,393	17	TGATGAGAATGATGAnG	CnTCATCATTCTCATCA
0 annotated groups 2 'de novo' group(s) 1, 2071	1206	1.93E-01	CHROMOSOME_I:4,656,412-4,656,429	18	CGTTGAGAGATAAGGGAC	GTCCCTTATCTCTCAACG
1 annotated group(s): 40190 (SREBP-1) [2.02E-06] 1 'de novo' group(s) 75	1207	7.72E-01	CHROMOSOME_I:4,656,429-4,656,442	14	TTGAGAGAnAAGGG	CCCTTnTCTCTCAA
1 annotated group(s): 40190 (SREBP-1) [2.02E-06] 2 'de novo' group(s) 75, 3208	1208	1.28E-01	CHROMOSOME_I:4,656,435-4,656,451	17	GCATGGGGwGATGCTGA	TCAGCATCsCCCCATGC
0 annotated groups 0 'de novo' group(s)	1209	8.67E-02	CHROMOSOME_I:4,656,525-4,656,530	6	TCGCCG	CGGCGA
1 annotated group(s): 40054 (DeltaNp63alpha) [6.57E-06] 0 'de novo' group(s)	1210	1.28E-01	CHROMOSOME_I:4,656,544-4,656,560	17	GAAGGnCAmGAAGAAGA	TCTTCTTCkTGnCCTTC