Schema for Combined Splice Junctions (Cell Lines) - Combined Splice Junctions for Multiple Cell Lines
  Database: dm6    Primary Table: modENCODE_cells_junctions    Row Count: 168,655   Data last updated: 2021-09-01
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom chr2Lvarchar(255) values
chromStart 5972int(10) unsigned range
chromEnd 6312int(10) unsigned range
name JUNC00000010varchar(255) values
score 87int(10) unsigned range
strand +char(1) values
thickStart 5972int(10) unsigned range
thickEnd 6312int(10) unsigned range
itemRgb 2263842int(10) unsigned range
blockCount 2int(10) unsigned range
blockSizes 98,65longblob  
chromStarts 0,275longblob  

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEnditemRgbblockCountblockSizeschromStarts
585chr2L59726312JUNC0000001087+5972631234,139,34298,650,275
585chr2L59737586JUNC0000001111+5973758651,102,255297,130,1600
585chr2L61957665JUNC00000012132+61957665192,96,154292,920,1378
585chr2L62477644JUNC000000135+624776440,0,0265,710,1326
585chr2L67287661JUNC000000147+672876610,0,0280,880,845
585chr2L76558076JUNC0000001615-7655807651,102,255299,970,324
585chr2L78118077JUNC000000174+781180770,0,0299,980,168
585chr2L80218286JUNC00000018283+80218286192,96,154295,940,171
585chr2L80398251JUNC000000194+803982510,0,0277,230,189
585chr2L1081218396JUNC000000904-10812183960,0,0299,660,7518

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Combined Splice Junctions (Cell Lines) (modENCODE_cells_junctions) Track Description
 

Description

This track shows the exon junctions extracted from spliced RNA-Seq reads of D. melanogaster cell lines. The RNA-Seq reads were obtained from the ENCODE data portal at UCSC on August 2019, and then mapped against the D. melanogaster dm6 genome assembly using HISAT2.

The splice junctions in each sample were identified by the regtools junctions extract subprogram. The splice junction predictions from the different samples are filtered and merged together into a single set of predictions. The predictions are color-coded based on the number of reads supporting the junction:

ColorNumber of reads
> 1000
500-999
100-499
50-99
10-49
< 10

References

Cherbas L, et al. The transcriptional diversity of 25 Drosophila cell lines.. Genome Res. 2011 Feb;21(2):301-14.

Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015 Apr;12(4):357-60.