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

gtacaatgcctgctaggttgcgctgtgatcactcatactctccaaaggactatcttgcattaaactagctgtagtaatttttgcctcgtcgtttatgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGACAGCGAGGACATGGAGGAGGAAATTGAAGAGGAGGTTGACAAGGTCCTCA

Basic information

species	Zea mays
transcript	GRMZM2G042552_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G042552_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g01810.1 (Oryza sativa), 3'ss of exon 4

gtacaatgcctgctaggttgcgctgtgatcactcatactctccaaaggactatcttgcattaaactagctgtagtaatttttgcctcgtcgtttatgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGACAGCGAGGACATGGAGGAGGAAATTGAAGAGGAGGTTGACAAGGTCCTCA
             | | ||  |   |||||||  ||    ||||||||  | |||||   |  | |  |  || || || || | || |  ||  |||||||||||||||||| |||||||||||||| ||||||||| | |||||| |||||||||  |||||||| |||||||| ||||||||||||||||||||||||||| 
----------gtatggattatgaaatgatcac--atctcttccaaaggtttttcttgtcctgta-tgcccatactagttcttacttcctgattgctgtggtgtagGCTGGTGTAATGGAAGAAATGGTGAACGATGCTGTGGATTCAGCGCTGGACAATGAGGACATTGAGGAGGAGATTGAAGAGGAGGTTGACAAGGTCCTCT

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|87154823|gb|DY399612.1|DY399612

EST:     CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
genomic: CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC

EST: gi|44901356|gb|CK827901.1|CK827901

EST:     CCCCGGAGGTTGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACTCTGGAC
genomic: CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC

EST: gi|32834245|gb|CD973923.1|CD973923

EST:     CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAATGCTGGAC
genomic: CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC

EST: gi|14255660|gb|BG878568.1|BG878568

EST:     CCCCCGAGGTCGCAGCCTCAATGCAGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
genomic: CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC

EST: gi|113702321|gb|EE679825.1|EE679825

EST:     CCCCGGAGGTTGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACTCTGGAC
genomic: CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC

EST: gi|4646886|gb|AI621961.1|AI621961

EST:     AGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
genomic: AGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC

EST: gi|21759932|gb|BQ635473.1|BQ635473

EST:     AGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACTCTGGAC
genomic: AGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC

EST: gi|60399737|gb|DN232547.1|DN232547

EST:     CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
genomic: CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC

EST: gi|14311555|gb|BG901310.1|BG901310

EST:     CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
genomic: CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC

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: 49 (upstream exon), 49 (downstream exon)
Score: 171

CTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGACAGCGAGGACATGGAGGAGGAAATTGAAGAGGAGGTTGACAAGGTCCTCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tatcttgcattaaactagctgtagtaatttttgcctcgtcgtttatgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGACAGCGAGGACATGGAGGAGGAAATTGAAGAGGAGGTTGACAAGGTCCTCA

                     tagtaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaatgcctgctaggttgcgctgtgatcactcatactctccaaaggactatcttgcattaaactagctgtagtaatttttgcctcgtcgtttatgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGACAGCGAGGACATGGAGGAGGAAATTGAAGAGGAGGTTGACAAGGTCCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG