Region for Gene B0041.3

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 42 out of 42 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)	1212	8.22E-01	CHROMOSOME_I:4,644,059-4,644,068	10	TGTTTGCACy	rGTGCAAACA
0 annotated groups 2 'de novo' group(s) 59, 278	1211	9.54E-01	CHROMOSOME_I:4,644,061-4,644,072	12	kTyGAACCmyGw	sCrkGGTTCrAm
0 annotated groups 0 'de novo' group(s)	1213	9.19E-01	CHROMOSOME_I:4,644,067-4,644,076	10	AmCCCTGAAA	TTTCAGGGkT
5 annotated group(s): 50029 (Evi-1) [1.27E-06] 40073 (Evi-1) [2.02E-06] 40073 (Evi-1) [3.03E-06] ... 2 'de novo' group(s) 1, 604	1214	6.62E-01	CHROMOSOME_I:4,644,078-4,644,093	16	nACTTATCTTATCnTT	AAnGATAAGATAAGTn
1 annotated group(s): 30010 (ELT-2) [1.12E-04] 1 'de novo' group(s) 1	1215	8.22E-01	CHROMOSOME_I:4,644,121-4,644,130	10	GATAAGwTnA	TnAsCTTATC
0 annotated groups 0 'de novo' group(s)	1216	8.32E-01	CHROMOSOME_I:4,644,136-4,644,153	18	AAGGmAkAkAAwAAArns	wnyTTTsTTmTmTkCCTT
1 annotated group(s): 50047 (HNF-3beta) [8.05E-05] 0 'de novo' group(s)	1221	7.01E-01	CHROMOSOME_I:4,644,160-4,644,173	14	TTTTTmTmTGCCTT	AAGGCAkAkAAAAA
1 annotated group(s): 50047 (HNF-3beta) [8.05E-05] 0 'de novo' group(s)	1217	7.57E-01	CHROMOSOME_I:4,644,164-4,644,175	12	TTTTTGsTTTAA	TTAAAwCAAAAA
1 annotated group(s): 50047 (HNF-3beta) [8.05E-05] 0 'de novo' group(s)	1219	8.40E-01	CHROMOSOME_I:4,644,167-4,644,176	10	wTGsTTTAAm	kTTAAAwCAs
0 annotated groups 0 'de novo' group(s)	1222	3.16E-01	CHROMOSOME_I:4,644,178-4,644,183	6	TATATT	AATATA
1 annotated group(s): 50101 (c-REL) [5.63E-05] 0 'de novo' group(s)	1223	9.08E-01	CHROMOSOME_I:4,644,214-4,644,231	18	ynynnTTTyTCCTTTTTy	rAAAAAGGArAAAnnrnr
0 annotated groups 0 'de novo' group(s)	1224	2.26E-01	CHROMOSOME_I:4,644,265-4,644,272	8	ArrCAAAT	ATTTGyyT
1 annotated group(s): 50070 (Pbx) [2.50E-05] 0 'de novo' group(s)	1225	9.55E-01	CHROMOSOME_I:4,644,304-4,644,317	14	AnTwnTCGrTAATk	mATTAyCGAnsAnT
0 annotated groups 0 'de novo' group(s)	1226	6.90E-01	CHROMOSOME_I:4,644,316-4,644,323	8	TkTyTGCr	yGCArAmA
0 annotated groups 0 'de novo' group(s)	1227	9.08E-01	CHROMOSOME_I:4,644,326-4,644,333	8	wTATATGC	GCATATAs
0 annotated groups 0 'de novo' group(s)	1228	3.52E-01	CHROMOSOME_I:4,644,331-4,644,338	8	yGCAAAmA	TkTTTGCr
0 annotated groups 0 'de novo' group(s)	1229	9.89E-01	CHROMOSOME_I:4,644,337-4,644,360	24	AAGrCAkAkAAAAAArA...	TsCAynkTyTTTTTTmT...
0 annotated groups 2 'de novo' group(s) 2850, 2075	1231	9.93E-01	CHROMOSOME_I:4,644,364-4,644,383	20	AGTGCAAACAnAAnAAmnGA	TCnkTTnTTnTGTTTGCACT
0 annotated groups 0 'de novo' group(s)	1230	9.10E-01	CHROMOSOME_I:4,644,365-4,644,376	12	GTknAAmCATrA	TyATGkTTnmAC
1 annotated group(s): 40034 (CAC-binding_protein) [5.80E-06] 4 'de novo' group(s) 4, 33, 43, 674	1233	9.50E-01	CHROMOSOME_I:4,644,380-4,644,403	24	AwnACrCsCGATyrmkT...	nnAwnwGAmkyrATCGw...
0 annotated groups 1 'de novo' group(s) 43	1232	9.86E-01	CHROMOSOME_I:4,644,381-4,644,390	10	TGACnCCTGA	TCAGGnGTCA
0 annotated groups 0 'de novo' group(s)	1234	7.42E-01	CHROMOSOME_I:4,644,405-4,644,414	10	CCACTTCTCC	GGAGAAGTGG
2 annotated group(s): 40147 (NRSF) [7.59E-06] 50014 (Bsap) [4.62E-05] 0 'de novo' group(s)	1235	8.49E-01	CHROMOSOME_I:4,644,417-4,644,438	22	yTmTTTsGCATATTyyC...	mrwAAGrrAATATGCwA...
3 annotated group(s): 40147 (NRSF) [7.59E-06] 40154 (Pax-5) [8.32E-06] 50014 (Bsap) [4.62E-05] 2 'de novo' group(s) 63, 77	1236	9.28E-01	CHROMOSOME_I:4,644,434-4,644,450	17	TTCyGCGCCTGGGCCnm	knGGCCCAGGCGCrGAA
3 annotated group(s): 40154 (Pax-5) [8.32E-06] 50048 (Hen-1) [4.55E-05] 50014 (Bsap) [6.21E-05] 1 'de novo' group(s) 22	1237	6.00E-01	CHROMOSOME_I:4,644,449-4,644,469	21	ymCAsCCGAATTGATCG...	CAyGCGATCAATTCGGw...
0 annotated groups 1 'de novo' group(s) 49	1238	9.53E-01	CHROMOSOME_I:4,644,479-4,644,488	10	CCAGyGArAG	CTyTCrCTGG
0 annotated groups 0 'de novo' group(s)	1239	6.75E-01	CHROMOSOME_I:4,644,489-4,644,495	7	wGTGTAT	ATACACs
0 annotated groups 0 'de novo' group(s)	1240	2.56E-01	CHROMOSOME_I:4,644,499-4,644,506	8	TCyCTTTT	AAAAGrGA
0 annotated groups 0 'de novo' group(s)	1241	6.60E-01	CHROMOSOME_I:4,644,508-4,644,525	18	yknmCwTTTCTCCTTTTy	rAAAAGGAGAAAsGknmr
0 annotated groups 0 'de novo' group(s)	1242	8.37E-01	CHROMOSOME_I:4,644,529-4,644,540	12	ynTCTCCTynTy	rAnrAGGAGAnr
0 annotated groups 0 'de novo' group(s)	1243	8.49E-01	CHROMOSOME_I:4,644,539-4,644,554	16	wwGTGwwTTAnwAwAw	sTsTsnTAAssCACss
0 annotated groups 0 'de novo' group(s)	1244	4.40E-01	CHROMOSOME_I:4,644,563-4,644,572	10	TArAwCAsTw	sAwTGsTyTA
0 annotated groups 0 'de novo' group(s)	1245	9.39E-01	CHROMOSOME_I:4,644,572-4,644,587	16	TTnTATAAATATAnGn	nCnTATATTTATAnAA
0 annotated groups 0 'de novo' group(s)	1246	9.53E-01	CHROMOSOME_I:4,644,616-4,644,626	11	nTTAAACCATr	yATGGTTTAAn
0 annotated groups 0 'de novo' group(s)	1247	9.08E-01	CHROMOSOME_I:4,644,617-4,644,624	8	TTAAACCA	TGGTTTAA
0 annotated groups 0 'de novo' group(s)	1249	9.96E-01	CHROMOSOME_I:4,644,617-4,644,628	12	TTrAAsmATAAw	sTTATkwTTyAA
0 annotated groups 0 'de novo' group(s)	1250	9.97E-01	CHROMOSOME_I:4,644,619-4,644,632	14	nGATAAGATwAkTn	nAmTsATCTTATCn
0 annotated groups 1 'de novo' group(s) 12	1251	9.94E-01	CHROMOSOME_I:4,644,631-4,644,644	14	TTwAAACCATrAAT	ATTyATGGTTTsAA
0 annotated groups 0 'de novo' group(s)	1252	5.38E-01	CHROMOSOME_I:4,644,636-4,644,646	11	GCGATCAwTTC	GAAsTGATCGC
0 annotated groups 0 'de novo' group(s)	1253	5.26E-01	CHROMOSOME_I:4,644,646-4,644,661	16	CArTrAAAAmGGAGAr	yTCTCCkTTTTyAyTG
0 annotated groups 0 'de novo' group(s)	1254	7.95E-01	CHROMOSOME_I:4,644,659-4,644,668	10	GAACsAyGAw	sTCrTwGTTC
1 annotated group(s): 50069 (Pax6) [3.90E-05] 0 'de novo' group(s)	1255	3.63E-01	CHROMOSOME_I:4,644,666-4,644,679	14	GTTrAACCATGAAT	ATTCATGGTTyAAC