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

...gtaatcagctggtgtcaagtgggaaacttcccagcattttttcttttgtttctttttgaatggtcttttggttcatccggtagtgacctatttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTCACAGTGATAATTTGGCGAACTATGGAAAGTTATGTCGTGAAAGAACACA

Basic information

species	Zea mays
transcript	GRMZM2G049091_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G049091_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g43450.1 (Oryza sativa), 3'ss of exon 2

gtaatcagctggtgtcaagtgggaaacttcccagcatttttt--cttttgtttctttttgaatggtcttttggttcatccggtagtgacct--atttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTCACAGTGATAATTTGGCGAACTATGGAAAGTTATGTCGTGAAAGAACACA
 ||   |  |  | | |      | | ||    | || |||    |||   |    | | |   || ||     ||| ||   | ||||||   | ||||| ||||||||||||||| |||||||||||||||||||||||||||||| | ||||||||||||||||||| |||||||||||||||||| |||||||| |||||
-tatggattttttattactacttacatttttggggatctttcaagtttcaatagcatctaa---gttttgactatcacccaaaaatgacctttgtgtgttgtagGGAAACTTTCATGTGAAGGAAAAGTCGAGCATAAATTTGACATGAAGCCTCACAGTGATAATTTGGTGAACTATGGAAAGTTATGCCGTGAAAGGACACA

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|149087889|gb|EE177157.2|EE177157

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|60394867|gb|DN227736.1|DN227736

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|71321698|gb|DR797541.1|DR797541

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|211472635|gb|FL331977.1|FL331977

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGGAAACTTTCAT
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGG-AAACTTTCAT

EST: gi|71330940|gb|DR802278.1|DR802278

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|149087888|gb|EE287172.2|EE287172

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|149111893|gb|EE191049.2|EE191049

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|148942185|gb|EC887190.2|EC887190

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|211306084|gb|FL334837.1|FL334837

EST:     TATGTTCNAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|148999712|gb|EE036711.2|EE036711

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|74242554|gb|DT650468.1|DT650468

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|91869046|gb|EB400256.1|EB400256

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|60341247|gb|DN208220.1|DN208220

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|6307892|gb|AW163859.1|AW163859

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|211233734|gb|FL380048.1|FL380048

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCAAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

EST: gi|78083457|gb|DV511850.1|DV511850

EST:     TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAG                         GGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC
genomic: TATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTC

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: 47 (upstream exon), 48 (downstream exon)
Score: 125

GAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTACTCTTTGAATATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAATCTAACCAAGgtaggattca ... tttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTCACAGTGATAATTTGGCGAACTATGGAAAGTTATGTCGTGAAAGAACACA

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 93

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 95

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttctttttgaatggtcttttggttcatccggtagtgacctatttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTCACAGTGATAATTTGGCGAACTATGGAAAGTTATGTCGTGAAAGAACACA

                                         cctattt  CT-rich tract
       tttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcagctggtgtcaagtgggaaacttcccagcattttttcttttgtttctttttgaatggtcttttggttcatccggtagtgacctatttgttgcagGGAAACTTTCATGCGAAGGAAAAGTCGAGCATAAATTTGACATGGAACCTCACAGTGATAATTTGGCGAACTATGGAAAGTTATGTCGTGAAAGAACACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC