Region for Gene B0205.10

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 39 out of 39 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)	1428	9.78E-02	CHROMOSOME_I:10,707,331-10,707,340	10	AAGTGAArAG	CTyTTCACTT
0 annotated groups 0 'de novo' group(s)	1429	3.41E-01	CHROMOSOME_I:10,707,361-10,707,370	10	ATCCAGACGA	TCGTCTGGAT
1 annotated group(s): 50014 (Bsap) [4.62E-05] 0 'de novo' group(s)	1430	3.12E-01	CHROMOSOME_I:10,707,404-10,707,413	10	AAGTGAArAG	CTyTTCACTT
1 annotated group(s): 50014 (Bsap) [5.78E-05] 0 'de novo' group(s)	1431	1.12E-01	CHROMOSOME_I:10,707,430-10,707,435	6	AAGTCr	yGACTT
0 annotated groups 0 'de novo' group(s)	1432	3.54E-01	CHROMOSOME_I:10,707,507-10,707,514	8	GTCTGAAG	CTTCAGAC
0 annotated groups 1 'de novo' group(s) 23	1433	7.02E-01	CHROMOSOME_I:10,707,540-10,707,553	14	AAACGTnAACCwnn	nnsGGTTnACGTTT
0 annotated groups 0 'de novo' group(s)	1434	7.12E-01	CHROMOSOME_I:10,707,571-10,707,582	12	TGACTTTTnGTT	AACnAAAAGTCA
1 annotated group(s): 40024 (BHLHB2) [9.12E-06] 0 'de novo' group(s)	1435	9.99E-01	CHROMOSOME_I:10,707,647-10,707,660	14	GTTAAATCnnAGCG	CGCTnnGATTTAAC
1 annotated group(s): 40024 (BHLHB2) [9.12E-06] 0 'de novo' group(s)	1436	7.33E-01	CHROMOSOME_I:10,707,658-10,707,670	13	GCnwCTGrAGGTG	CACCTyCAGsnGC
0 annotated groups 0 'de novo' group(s)	1437	3.16E-01	CHROMOSOME_I:10,707,670-10,707,679	10	CGAAAAGTCA	TGACTTTTCG
0 annotated groups 0 'de novo' group(s)	1438	1.40E-01	CHROMOSOME_I:10,707,705-10,707,712	8	CTTTCAGA	TCTGAAAG
0 annotated groups 0 'de novo' group(s)	1439	2.20E-01	CHROMOSOME_I:10,707,731-10,707,740	10	TTCCAGAAGn	nCTTCTGGAA
0 annotated groups 0 'de novo' group(s)	1440	9.52E-01	CHROMOSOME_I:10,707,747-10,707,756	10	AkCnAAACGA	TCGTTTnGmT
0 annotated groups 0 'de novo' group(s)	1441	1.74E-01	CHROMOSOME_I:10,707,765-10,707,774	10	GAATCTGGAG	CTCCAGATTC
0 annotated groups 1 'de novo' group(s) 94	1442	7.30E-01	CHROMOSOME_I:10,707,800-10,707,810	11	TTnCAGwAACC	GGTTsCTGnAA
0 annotated groups 0 'de novo' group(s)	1443	4.74E-01	CHROMOSOME_I:10,707,807-10,707,818	12	AACnAAAAGTCA	TGACTTTTnGTT
0 annotated groups 0 'de novo' group(s)	1444	4.58E-01	CHROMOSOME_I:10,707,939-10,707,949	11	nAAyTTACCAA	TTGGTAArTTn
0 annotated groups 0 'de novo' group(s)	1445	1.00E-08	CHROMOSOME_I:10,707,950-10,707,955	6	AGCTTT	AAAGCT
0 annotated groups 0 'de novo' group(s)	1446	1.74E-01	CHROMOSOME_I:10,707,971-10,707,980	10	TTGGTAAGTT	AACTTACCAA
1 annotated group(s): 50027 (EN-1) [5.33E-05] 0 'de novo' group(s)	1447	4.74E-01	CHROMOSOME_I:10,708,186-10,708,191	6	TGGATC	GATCCA
0 annotated groups 0 'de novo' group(s)	1448	6.42E-01	CHROMOSOME_I:10,708,296-10,708,307	12	AACnAArAGyCA	TGrCTyTTnGTT
0 annotated groups 0 'de novo' group(s)	1449	9.27E-01	CHROMOSOME_I:10,708,314-10,708,327	14	CTAnTAAAAACGTG	CACGTTTTTAnTAG
0 annotated groups 0 'de novo' group(s)	1450	8.47E-01	CHROMOSOME_I:10,708,361-10,708,376	16	nnCGAAAAGTCrwnnn	nnnsyGACTTTTCGnn
0 annotated groups 0 'de novo' group(s)	1451	7.19E-01	CHROMOSOME_I:10,708,375-10,708,392	18	nTCnATGACTTTTCGnTT	AAnCGAAAAGTCATnGAn
3 annotated group(s): 40209 (XBP-1) [7.99E-06] 50065 (PPARgamma-RXRal) [4.22E-05] 50058 (Max) [4.87E-05] 5 'de novo' group(s) 2, 90, 610, 2717, 1829	1452	8.67E-01	CHROMOSOME_I:10,708,388-10,708,409	22	nmTTTCAGACACGTGTC...	ymAACGACACGTGTCTG...
1 annotated group(s): 50065 (PPARgamma-RXRal) [4.22E-05] 2 'de novo' group(s) 26, 655	1453	4.14E-01	CHROMOSOME_I:10,708,405-10,708,420	16	CGTTGACnGGTrAGTT	AACTyACCnGTCAACG
2 annotated group(s): 50058 (Max) [3.56E-05] 50107 (p65) [5.03E-05] 0 'de novo' group(s)	1454	1.40E-01	CHROMOSOME_I:10,708,450-10,708,457	8	GGTTTCCG	CGGAAACC
0 annotated groups 1 'de novo' group(s) 481	1455	9.63E-01	CHROMOSOME_I:10,708,486-10,708,503	18	ATCCAATAGATTGAnnnn	nnnnTCAATCTATTGGAT
0 annotated groups 0 'de novo' group(s)	1456	5.91E-01	CHROMOSOME_I:10,708,561-10,708,574	14	GAwAAGTCnTTGAn	nTCAAnGACTTsTC
0 annotated groups 0 'de novo' group(s)	1457	1.16E-01	CHROMOSOME_I:10,708,596-10,708,601	6	mGATTG	CAATCk
0 annotated groups 0 'de novo' group(s)	1458	5.29E-01	CHROMOSOME_I:10,708,599-10,708,613	15	kTGAACGAnAAGTGn	nCACTTnTCGTTCAm
0 annotated groups 0 'de novo' group(s)	1459	3.41E-01	CHROMOSOME_I:10,708,620-10,708,629	10	TCGTCTGGAT	ATCCAGACGA
0 annotated groups 0 'de novo' group(s)	1460	2.24E-01	CHROMOSOME_I:10,708,630-10,708,637	8	TmAACsAC	GTwGTTkA
1 annotated group(s): 50069 (Pax6) [6.54E-05] 0 'de novo' group(s)	1461	9.63E-01	CHROMOSOME_I:10,708,639-10,708,656	18	nnATCGTCyTnTGrATnn	nnATyCAnArGACGATnn
0 annotated groups 0 'de novo' group(s)	1462	7.96E-01	CHROMOSOME_I:10,708,675-10,708,690	16	nnrTCmAmsAAAnGTk	mACnTTTwkTkGAynn
1 annotated group(s): 50065 (PPARgamma-RXRal) [3.14E-05] 0 'de novo' group(s)	1463	1.00E-08	CHROMOSOME_I:10,708,695-10,708,700	6	AAAGCT	AGCTTT
0 annotated groups 0 'de novo' group(s)	1464	8.67E-01	CHROMOSOME_I:10,708,720-10,708,733	14	GCTAAATCTGAGCG	CGCTCAGATTTAGC
0 annotated groups 0 'de novo' group(s)	1465	5.35E-01	CHROMOSOME_I:10,708,779-10,708,794	16	nAnTTTCAGATTGAAA	TTTCAATCTGAAAnTn
0 annotated groups 0 'de novo' group(s)	1466	9.14E-02	CHROMOSOME_I:10,708,796-10,708,809	14	AACGAAAAGTCAkC	GmTGACTTTTCGTT