ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TTGCACTGCTGGTGGGGCATATATTCCTGCAATGGCGGATGAGAGTGTAATAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAGgtcagaatattctggaaccattttgtttattttctaaatgataaaattttggtgtctaaatctctaatatattaaagcaccggtcgtcccgcgtcaatat...

Basic information

species	Zea mays
transcript	GRMZM2G702490_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G702490_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g32850.2 (Oryza sativa), 5'ss of exon 2

TTGCACTGCTGGTGGGGCATATATTCCTGCAATGGCGGATGAGAGTGTAATAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAGgtcagaatattctgga-accattttgtttattttctaaatgataaa-attttggtgtct----aaatctctaatatattaaagcaccggtcgtcccgcgtcaatat
||| || |||||||| || |||||||| |||||||| ||||||||||||||||| ||||||||||| || ||||||||||| |||||||||||||||||||| ||  |  ||||    |||||||| |||||   |  ||| |    ||  ||   |||    || | || ||| | || ||  | ||    |   ||  ||||| 
TTGTACCGCTGGTGGTGCTTATATTCCGGCAATGGCTGATGAGAGTGTAATAGTAAAGGGAAATGGAACAATATTTCTAGCTGGTCCACCACTTGTAAAGgtgagtgttctctgcctgccattttgattattcattttatgttttgcatggtgagatcttgagaactatccaatgttttcaa--atcgcctat---gcaccaata-

upper sequence: GRMZM2G702490_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA07G33620.1 (Glycine max), 5'ss of exon 2

TTGCACTGCTGGTGGGGCATATATTCCTGCAATGGCGGATGAGAGTGTAATAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAGgtcagaatattctggaaccattttgtttattttctaaatgataaaattttggtgtctaaatctctaatatattaaagcaccggtcgtcccgcgt--caatat----------------------------------------------------------------------------
||||||||||||||| || ||||||||||| ||||| ||||| ||||| || || ||||||||||| || || ||| |||| || ||||| ||||| |||||  |      ||       |  |  | |  | ||   ||||||  | | | | | |  || |     || || ||   | | |  |      |  ||||||                                                                            
TTGCACTGCTGGTGGCGCTTATATTCCTGCTATGGCCGATGAAAGTGTGATGGTCAAGGGAAATGGCACCATTTTTTTAGCAGGGCCACCTCTTGTTAAGgtttgctctagctactcttgtact-ctaaaatactgtgtgataatctctggctatttctatgttcttgatttttaaaatctgtttcttttaaatttcaatattttaacactaacaatgtgtttgtgtattttctatgcatttataaccaaaattaaccttaattaaatgattttatag

upper sequence: GRMZM2G702490_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G14860.1 (Glycine max), 5'ss of exon 2

TTGCACTGCTGGTGGGGCATATATTCCTGCAATGGCGGATGAGAGTGTAATAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAGgtcagaatattctggaaccattttgttt----attttctaaatgataaaattttggtgtctaaat-ctctaatatattaaagcaccggtcgtcccg-cgtcaatat-----------------------------------------------------------------------------
||||||||||||||| || ||||||||||| ||||| ||||| ||||| || || ||||||||||| || || ||| |||| || ||||| ||||| ||||| ||    |   |  ||  || || |     || || |  |||||||  | | | | | |  ||  |||   || |||||  |    || |       |||||||                                                                             
TTGCACTGCTGGTGGCGCTTATATTCCTGCTATGGCTGATGAAAGTGTGATGGTCAAGGGAAATGGTACCATTTTTTTAGCAGGGCCACCTCTTGTTAAGgttagc---tctagctactcttgtgctccaaaatgttttgtatgataatctctggctatttctatgttcttgaattttaaaatatgtttcttttaaatttcaatattttgacattaacaatgtgttgatgtattttttatgcatttatgaccaaaattaaaccttaattaaatgattttttag

upper sequence: GRMZM2G702490_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT4G34030.1 (Arabidopsis thaliana), 5'ss of exon 3

TTGCACTGCTGGTGGGGCATATATTCCTGCAATGGCGGATGAGAGTGTAATAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAGgtcagaatattctggaaccattttgtttattt-tctaaatgataaaattttggtgtctaaatctctaatatattaaagcaccggtcgtcccgcgtcaatat--
 |||||||||||||| || || |||||||| ||||| ||||| |||||||| || || || ||||| || |||||| |||| || || |||||||| |||||||  || ||||  |   | ||| | | | | |||   |  |   | | |   ||   | | |||     ||  ||       |      || |    |   
CTGCACTGCTGGTGGTGCCTACATTCCTGCCATGGCTGATGAAAGTGTAATGGTCAAAGGGAATGGTACCATATTTTTAGCAGGACCGCCACTTGTCAAGgtca--attttctcaagttactttctctctctctctctctcgttctagtcttaagt---agtttcttgagaatctaacgctaaatgaaaaagcttttgaacag

upper sequence: GRMZM2G702490_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv03s0063g00290.t01 (Vitis vinifera), 5'ss of exon 3

TTGCACTGCTGGTGGGGCATATATTCCTGCAATGGCGGATGAGAGTGTAATAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAGgtcagaatattctggaaccattttgtttattttctaaatgataaaattttggtgtctaaatctctaatatatta---aagcaccggtcgtcccgcgtcaatat-------
||| ||||||||||| || ||||| ||||||||||||||||| ||||| || || || |||||||| || ||||||||||| || || |||||||| ||||| ||    |||  || |  |||||     |  ||||||| |  |  |   ||| ||  ||   ||||   ||    | |    |   ||  |  |   |  |       
TTGTACTGCTGGTGGTGCTTATATACCTGCAATGGCGGATGAAAGTGTTATGGTCAAAGGAAATGGTACCATATTTCTAGCTGGGCCTCCACTTGTGAAGgttag----ttccagatc--ttttggca--tgcctaaatgcttca--tgcagtggctggattcataattctttttgcatgttttgcatgtttcctgaagaattataaaaa

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|60341832|gb|DN208805.1|DN208805

EST:     TAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAG                         GCTGCTACAGGAGAGGAGATATCTGCTGAGGACCTTGGTGGAGCATCAGTA
genomic: TAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAGgtcagaatat ... ttttttgtagGCTGCTACAGGAGAGGAGATATCTGCTGAGGACCTTGGTGGAGCATCAGTA

EST: gi|211125174|gb|FL001724.1|FL001724

EST:     TAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAG                         GCTGCTACAGGAGAGGAGATATCTGCTGAGGACCTTGGTGGAGCATCAGTA
genomic: TAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAGgtcagaatat ... ttttttgtagGCTGCTACAGGAGAGGAGATATCTGCTGAGGACCTTGGTGGAGCATCAGTA

EST: gi|211125176|gb|FL001726.1|FL001726

EST:     TAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAG                         GCTGCTACAGGAGAGGAGATATCTGCTGAGGACCTTGGTGGAGCATCAGTA
genomic: TAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAGgtcagaatat ... ttttttgtagGCTGCTACAGGAGAGGAGATATCTGCTGAGGACCTTGGTGGAGCATCAGTA

EST: gi|211125178|gb|FL001728.1|FL001728

EST:     TAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAG                         GCTGCTACAGGAGAGGAGATATCTGCTGAGGACCTTGGTGGAGCATCAGTA
genomic: TAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAGgtcagaatat ... ttttttgtagGCTGCTACAGGAGAGGAGATATCTGCTGAGGACCTTGGTGGAGCATCAGTA

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: 44 (upstream exon), 48 (downstream exon)
Score: 80

TTGCACTGCTGGTGGGGCATATATTCCTGCAATGGCGGATGAGAGTGTAATAGTTAAGGGAAATGGGACTATATTTCTAGCGGGTCCACCACTTGTAAAGgtcagaatat ... ttttttgtagGCTGCTACAGGAGAGGAGATATCTGCTGAGGACCTTGGTGGAGCATCAGTACATTGCAAGGTATCAGGAGTCTCAGATCATTTTGCACAAG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 411

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 246