ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CACCTGTGGAGGCCTCTGCCCGGGATTGAACACGGTCATCCGCGAGCTTGTTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccgaggagtttaatggtgttcgtcctgtgaaaaaacattgtttactagttaatttgaacatgttttttttaaaacaaagaataatccgagatc...

Basic information

species	Zea mays
transcript	GRMZM2G080375_T02
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G080375_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 5'ss of exon 4

CACCTGTGGAGGCCTCTGCCCGGGATTGAACACGGTCATCCGCGAGCTTGTTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccgaggagtttaatggtgttcgtcctgtgaaaaaacattgtttactagttaatttgaacatgttttttttaaaacaaa---gaataatccgagatc
|||||| || ||||||||||| ||| | ||||| || |||||||||||||| ||||||||||||||||||||||||||| |||||||||| |||||||||||||  | |  |   ||   | ||    |   |||| ||     || |||  | |  |   | ||||||||||      |    |   | | | |    ||  
CACCTGCGGTGGCCTCTGCCCTGGACTTAACACTGTTATCCGCGAGCTTGTGTGCGGCTTGTATGATATGTATGGCGTCACCAGCGTCGTTGGCATAGAGgtgattaacttgttcttattttgtcacggctttgtgtaacttagttctttgttggg-atgctaaacatgttttgggagtagttgatatgtacattttagga--

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|74234373|gb|DT642287.1|DT642287

EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG

EST: gi|116813643|gb|EC856113.1|EC856113

EST:     GGCGTCT-CAGCGTCGTCGGCATACAG                         GGTGGATACAA-GG-TTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: GGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG

EST: gi|148940563|gb|EC885365.2|EC885365

EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG

EST: gi|148941151|gb|EC886025.2|EC886025

EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTG

EST: gi|18661967|gb|BM501673.1|BM501673

EST:     TTGGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG

EST: gi|33099629|gb|CF059589.1|CF059589

EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAAGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCGAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG

EST: gi|76914829|gb|DV165709.1|DV165709

EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG

EST: gi|149087521|gb|EE176918.2|EE176918

EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG

EST: gi|76290797|gb|DV030365.1|DV030365

EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG

EST: gi|149111238|gb|EE294735.2|EE294735

EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG

EST: gi|76913985|gb|DV165359.1|DV165359

EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG

EST: gi|78078027|gb|DV506442.1|DV506442

EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTTGT-GCGTTGACACCAAA
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACT-GTTGCGTTGACACCAAA

EST: gi|148935767|gb|EC879810.2|EC879810

EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG

EST: gi|87153260|gb|DY398049.1|DY398049

EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG

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: 44

CACCTGTGGAGGCCTCTGCCCGGGATTGAACACGGTCATCCGCGAGCTTGTTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAGTCGGTGAACGACATCCATAAGAGAGGCGGGACTGTCCTCGGAACCTCAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 477

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 395

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCTGTGGAGGCCTCTGCCCGGGATTGAACACGGTCATCCGCGAGCTTGTTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccgaggagtttaatggtgttcgtcctgtgaaaaaacattgtttactagttaatttgaacatgttttttttaaaacaaagaataatccgagatc

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