ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CTCAACTACAACACGAATAGCTGCTGATCCTGATACACATCAAGATTTCGAGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacatgcagagatgagattcaagaatatttatattaaacattgaagcacctaacttgtgataaaactaggcataacctgaagcttattgatgtatctttttagctgccatctcttcttatcattttcttggtag

Basic information

species	Zea mays
transcript	GRMZM5G880300_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G880300_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g07950.1 (Oryza sativa), 5'ss of exon 3

CTCAACTACAACACGAATAGCTGCTGATCCTGATACACATCAAGATTTCGAGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacatgcagagatgagattcaagaatatttatattaaacattgaagcacctaacttgtgataaaactaggcataacctgaa-gcttattgatgtatcttt-ttagctgccatctcttcttatcattttcttggtag
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CTCAAGTTCAACACGAGTAGCTGCTGATCCTGATACACATCAAGATTTCCAGCCTACAAGCAAAAGTTCCAACATGTCTTTTGATGACATTGTTGCTCAGgtattaacatttataaatggatttttggaatatttaaattgatga--gatgagcttattttctagaaaggctaggcatatcttaaatgtttcattttgtgtttctgccatttgttaatgctacaacacaatcattgggcag

upper sequence: GRMZM5G880300_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g34620.9 (Oryza sativa), 5'ss of exon 3

CTCAACTACAACACGAATAGCTGCTGATCCTGATACACATCAAGATTTCGAGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacatgcagagatgagattcaagaatatttatattaaacattgaagcacctaacttgtgataaaactaggcataacctgaagcttattgatgtatcttt-ttagctgccatctcttcttatcattttcttggtag
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CTCAAGTTCAACACGAGTTGCTGCTGATCCTGATACACATCAAGATTTCCAGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacatttctaaatgagctttttggacatttaaatt-------gaagaacttattttgtggcaaagctaggcatgtcttaaagtttcatgatgtatttctgccatttgttaatgctgcctcataattgttgggcag

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|211324031|gb|FL418314.1|FL418314

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGTGNGAACCCAGTCTTGATCTACATGAAGGGT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAG-GAGAACCCAGTCTTGATCTACATGAAGGGT

EST: gi|211071256|gb|FL399022.1|FL399022

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

EST: gi|74236784|gb|DT644698.1|DT644698

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

EST: gi|211479938|gb|FL425914.1|FL425914

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

EST: gi|91877551|gb|EB407508.1|EB407508

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

EST: gi|211159736|gb|FL393706.1|FL393706

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATG
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATG

EST: gi|93017644|gb|EB643164.1|EB643164

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

EST: gi|76281315|gb|DV020883.1|DV020883

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

EST: gi|211148655|gb|FL387728.1|FL387728

EST:     AGCCAAAGAGCAGAATTTCARACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

EST: gi|211243072|gb|FL400459.1|FL400459

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

EST: gi|84980275|gb|DW530624.1|DW530624

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

EST: gi|211069174|gb|FL417736.1|FL417736

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

EST: gi|101389214|gb|EB816562.1|EB816562

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

EST: gi|93017643|gb|EB643163.1|EB643163

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

EST: gi|84980198|gb|DW530547.1|DW530547

EST:     AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAG                         GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT
genomic: AGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCT

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: 41 (upstream exon), 47 (downstream exon)
Score: 27

CTCAACTACAACACGAATAGCTGCTGATCCTGATACACATCAAGATTTCGAGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacat ... ttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 26

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 46

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 28

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCAACTACAACACGAATAGCTGCTGATCCTGATACACATCAAGATTTCGAGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacatgcagagatgagattcaagaatatttatattaaacattgaagcacctaacttgtgataaaactaggcataacctgaagcttattgatgtatctttttagctgccatctcttcttatcattttcttggtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG