ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtaactggtgaccattcctaatatttcttttttgcatttcgggaagcaaacatccattaatgttcccctgttttgtttgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTC

Basic information

species	Zea mays
transcript	GRMZM2G151268_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G151268_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g01170.1 (Oryza sativa), 3'ss of exon 3

gtaactggtgaccattcctaatatttcttttttgcat-ttcgggaagcaaacatccattaatgttccc------------ctgttttgtttgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTC
||||| | |  ||||  || |||  ||||   || || |     ||   ||||||   ||||| | |             |||||   |||||| ||||||| ||||||||||||||||||||| | || || || ||||||||||| |||||||||||||||||||||||||||||||||||  ||||| |||||||||
gtaacagtttgccatatctcataaatcttggatggatatgtccaaaatcaacatctgctaatgctgctattgattgttggctgttgcatttgtaaatcagCCAAAGGACTTCTGGAAGAATGAATTAAAGGATTTTTCTAACAAAAGCGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCCATGCTTCTAGATGTTC

upper sequence: GRMZM2G151268_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 3'ss of exon 3

gtaactggtgaccattcctaatatttcttttttgcat-ttcgggaagcaaacatccattaatgttccc------------ctgttttgtttgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTC
||||| | |  ||||  || |||  ||||   || || |     ||   ||||||   ||||| | |             |||||   |||||| ||||||| ||||||||||||||||||||| | || || || ||||||||||| |||||||||||||||||||||||||||||||| ||  ||||| |||||||||
gtaacagtttgccatatctcataaatcttggatggatatgtccaaaatcaacatctgctaatgctgctattgattgttggctgttgcatttgtaaatcagCCAAAGGACTTCTGGAAGAATGAATTAAAGGATTTTTCTAACAAAAGCGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGCCCCATGCTTCTAGATGTTC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|211533622|gb|FL412539.1|FL412539

EST:     GGGCGCAATTWAGTCACACAATGAWAGTTTACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGG
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGG

EST: gi|9028689|gb|BE238729.1|BE238729

EST:     GGGCGCAATTAAGTCACACAATGAAAGTT-ACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGGAAG
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAG

EST: gi|211029306|gb|FL370361.1|FL370361

EST:     GGGCGCAATTAAGTCACACAATGAA-GTTTACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGGAAGAATGAACTGATAGACTTCTCT
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCT

EST: gi|211511056|gb|FL378831.1|FL378831

EST:     GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAMC-TG                         CCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAAC
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAAC

EST: gi|29945213|gb|CB815527.1|CB815527

EST:     GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGA
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGA

EST: gi|74239381|gb|DT647295.1|DT647295

EST:     GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGA
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGA

EST: gi|211355840|gb|FL403701.1|FL403701

EST:     GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGT
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGT

EST: gi|211317656|gb|FL416767.1|FL416767

EST:     GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAMC-TG                         CCCAAGGACTTCTGGAAGAATGAACTGAAAGA
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGA

EST: gi|211156585|gb|FL395419.1|FL395419

EST:     GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGA
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGA

EST: gi|74239382|gb|DT647296.1|DT647296

EST:     GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTG                         CCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGA
genomic: GGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGA

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 29 (upstream exon), 49 (downstream exon)
Score: 148

GTAGGTTACTAACTGCACTTGTTTGCGAATACTTGGAGTGGGCGCAATTAAGTCACACAATGAAAGTTTACTTGCCAGAGTGTAACCTGgtaactggtg ... tgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTC

Block sizes: 29 (upstream exon), 48 (downstream exon)
Score: 83

Block sizes: 29 (upstream exon), 49 (downstream exon)
Score: 113

Block sizes: 29 (upstream exon), 43 (downstream exon)
Score: 82

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgcatttcgggaagcaaacatccattaatgttcccctgttttgtttgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTC

                      cattaat  putative branch site (score: 82)
                              ttcccctgttttgttt  CT-rich tract
                                      ttttgtttgtatat  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactggtgaccattcctaatatttcttttttgcatttcgggaagcaaacatccattaatgttcccctgttttgtttgtatatcagCCCAAGGACTTCTGGAAGAATGAACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG