Region for Gene ENSRNOG00000000805 (Uniprot/SWISSPROT: Gja1)

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 Rat genome assembly from Jun 2003. (UCSC rn3, RGSC 3.1, Ensembl v22) 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 34 out of 34 atomic motifs.

Group(s) crtRnor#(name) [p-value]	Motif craRnor#	Discovery p-value	Location	Width	(+)motif	(-)motif
0 annotated groups 0 'de novo' group(s)	36521	1.15E-01	chr20:35,421,505-35,421,516	12	TTwAAATTTGCT	AGCAAATTTsAA
0 annotated groups 0 'de novo' group(s)	36575	1.25E-01	chr20:35,421,953-35,421,962	10	nyTTTAAATA	TATTTAAArn
0 annotated groups 0 'de novo' group(s)	36623	2.22E-01	chr20:35,422,122-35,422,133	12	ACTryAAnTTTw	sAAAnTTryAGT
0 annotated groups 1 'de novo' group(s) 9242	36693	1.07E-01	chr20:35,422,207-35,422,218	12	TTCmCTTCTTTw	sAAAGAAGkGAA
0 annotated groups 0 'de novo' group(s)	36726	7.54E-02	chr20:35,422,682-35,422,695	14	ksAyATAAAGTTGn	nCAACTTTATrTwm
0 annotated groups 1 'de novo' group(s) 2167	36762	1.62E-01	chr20:35,422,718-35,422,725	8	GGAGGAGG	CCTCCTCC
0 annotated groups 1 'de novo' group(s) 6955	36854	1.14E-01	chr20:35,422,840-35,422,851	12	ATTwArATGAwA	TsTCATyTsAAT
0 annotated groups 0 'de novo' group(s)	36804	1.07E-01	chr20:35,422,844-35,422,855	12	AAAknGTAAnTT	AAnTTACnmTTT
0 annotated groups 1 'de novo' group(s) 11883	36898	1.08E-01	chr20:35,422,845-35,422,856	12	AAwGmAAAATTG	CAATTTTkCsTT
0 annotated groups 0 'de novo' group(s)	36943	7.80E-02	chr20:35,422,846-35,422,857	12	ATGnwAAATTGT	ACAATTTsnCAT
0 annotated groups 0 'de novo' group(s)	36974	7.90E-02	chr20:35,422,847-35,422,858	12	wGmAAAATTGTw	sACAATTTTkCs
0 annotated groups 0 'de novo' group(s)	37002	7.44E-02	chr20:35,422,850-35,422,863	14	TTACTTGTTGGCnw	snGCCAACAAGTAA
0 annotated groups 1 'de novo' group(s) 11883	37033	9.33E-02	chr20:35,422,919-35,422,930	12	CAATGTTTCAnT	AnTGAAACATTG
0 annotated groups 0 'de novo' group(s)	37073	1.03E-01	chr20:35,423,003-35,423,012	10	AAAACTTACT	AGTAAGTTTT
0 annotated groups 1 'de novo' group(s) 6305	37103	2.23E-01	chr20:35,423,098-35,423,111	14	CCTTTGTTAATTGT	ACAATTAACAAAGG
0 annotated groups 1 'de novo' group(s) 14259	37150	7.82E-02	chr20:35,423,237-35,423,252	16	TTTGTTwATTGTCyTT	AArGACAATsAACAAA
0 annotated groups 1 'de novo' group(s) 11679	37193	1.13E-01	chr20:35,423,255-35,423,267	13	CTTTCATTwrGrG	CyCysAATGAAAG
0 annotated groups 0 'de novo' group(s)	37259	6.01E-02	chr20:35,423,294-35,423,302	9	CCCTCCnCC	GGnGGAGGG
0 annotated groups 1 'de novo' group(s) 2133	37337	5.49E-03	chr20:35,423,342-35,423,347	6	ATTTTA	TAAAAT
0 annotated groups 0 'de novo' group(s)	37417	1.16E-01	chr20:35,423,440-35,423,451	12	AACTTkATmTyk	mrAkATmAAGTT
0 annotated groups 1 'de novo' group(s) 12919	37857	1.31E-01	chr20:35,423,554-35,423,569	16	AGTTGAGTCAGTGGCT	AGCCACTGACTCAACT
0 annotated groups 1 'de novo' group(s) 3705	37465	5.49E-03	chr20:35,423,556-35,423,563	8	TTGAGTCA	TGACTCAA
0 annotated groups 0 'de novo' group(s)	37529	5.49E-03	chr20:35,423,556-35,423,565	10	TTGAGTCAGT	ACTGACTCAA
0 annotated groups 0 'de novo' group(s)	37610	5.49E-03	chr20:35,423,557-35,423,566	10	TGAGTCAGTG	CACTGACTCA
0 annotated groups 1 'de novo' group(s) 5377	37688	5.49E-03	chr20:35,423,558-35,423,565	8	GAGTCAGT	ACTGACTC
0 annotated groups 0 'de novo' group(s)	37768	5.49E-03	chr20:35,423,561-35,423,570	10	TCAGTGGCTT	AAGCCACTGA
0 annotated groups 0 'de novo' group(s)	38426	5.49E-03	chr20:35,423,566-35,423,588	23	GGCTTGAAACTTTTAAA...	AGAGCTTTTAAAAGTTT...
0 annotated groups 0 'de novo' group(s)	37929	5.49E-03	chr20:35,423,570-35,423,577	8	TGAAACTT	AAGTTTCA
0 annotated groups 1 'de novo' group(s) 167	38013	5.49E-03	chr20:35,423,574-35,423,581	8	ACTTTTAA	TTAAAAGT
0 annotated groups 1 'de novo' group(s) 5273	38106	5.49E-03	chr20:35,423,575-35,423,580	6	CTTTTA	TAAAAG
0 annotated groups 1 'de novo' group(s) 5103	38196	5.49E-03	chr20:35,423,576-35,423,581	6	TTTTAA	TTAAAA
0 annotated groups 1 'de novo' group(s) 5103	38276	5.49E-03	chr20:35,423,578-35,423,583	6	TTAAAA	TTTTAA
0 annotated groups 1 'de novo' group(s) 7116	38349	5.49E-03	chr20:35,423,579-35,423,586	8	TAAAAGCT	AGCTTTTA
0 annotated groups 1 'de novo' group(s) 10784	38497	5.49E-03	chr20:35,423,593-35,423,607	15	TCCAAGTwAGAAAAA	TTTTTCTsACTTGGA