ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtagtgctcactgctcagtcattttgatgaagaaggattctaggatacaatatgagctctatgctttggaaacatttctgcatgggattttttaattaatttctcccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC

Basic information

species	Zea mays
transcript	GRMZM2G006429_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g18970.1 (Oryza sativa), 3'ss of exon 3

gtagtgctcactgctcagtcattttgatgaagaaggattctaggatacaatatgagctctatgctttggaaacatttctg--catgggattttttaattaatttctccctt-ttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC
     |    |||||     || ||  || | |    ||| ||||||||        || ||||| |  || |||||||    ||||| |||  |    ||| |  |  || ||||||||||| |||||| ||||||||||||||||||||||||||||||| || |||||||||||||| || || ||||||||||| || ||||||||||||||||
-----gtaagctgctagtaaatattcttggaaagaacttcaaggataca-------ttcaatgctgtcaaagcatttctcattatgggttttgatgtgaaatcttgctgttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGC

upper sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G41810.2 (Glycine max), 3'ss of exon 4

gtagtgctcactgctcagtcattttgatgaagaaggattctaggatacaatatgagctctatgctttggaaacatttctgcatgggattttttaattaatttctccct---tttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC
                                        || ||| ||||   | |  | ||||||  ||  |    ||| |    ||  |   ||   ||  |  |   ||| ||||| || ||||| || ||||||||||||||||||||||| || || || || || || || || || || || || ||||| || || |||||||| ||||
---------------------------------------gtatgatgcaat--caccattgtgctttctaataaagattgcttaaacttagtagttttggtttgctttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCTAGATCTATAGGTGACACAGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC

upper sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G29060.1 (Glycine max), 3'ss of exon 4

gtagtgctcactgctcagtcattttgatgaagaaggattctaggatacaatatgagct--ctatgctttggaaac----atttctgcatgggattttttaattaatttctcccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC
                                             |||||| | | ||  |||| | ||   ||     | || | ||   |  | |||   |   ||    | | | ||||| || ||||| || || ||||| ||||||||||||||||| || |||||||| || || || || || || || ||||| || || |||||||||||||
--------------------------------------------gtacaatgtaatctttctattcctttctaatcaggactttttcactagcctgttttggttccttaatacatctatagGTAGGGCCTCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACAGACGTGGGAGAATTTATTGTCCCAATACCACATGTCAAGC

upper sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G38270.1 (Glycine max), 3'ss of exon 4

gtagtgctcactgctcagtcattttgatgaagaaggattctaggatacaatatgagctctatgctttggaaacatttctgcatgggattttttaattaatttctcccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC
                                      | | |  ||   | |    ||  | ||    |    ||| |   | |  | ||||  ||  ||  | | ||| | |||| || ||||| || |||||||| ||||||||||||||||| || |||||||| || || || || || || || ||||| || || |||||||| ||||
-------------------------------------gtatggtgtaatctttatattcctttctaatcaggactttttaactagcctgttttggttccttaatacatttat-agGTAGGGCCTCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC

upper sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G39260.1 (Glycine max), 3'ss of exon 4

gtagtgctcactgctcagtcattttgatgaagaaggattctaggatacaatatgagctctatgctttggaaacatttctgcatgggattttttaattaatttctcccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC
                      | ||||| |      || |  | |     |||   ||||    |    |   |||   | | | | ||||   ||   || |    ||| ||||| || ||||| || ||||||||||||||||||||||| || || ||||| || || || ||||| || || || ||||| || || |||||||| ||||
---------------------gtatgatgcaatcaccttttgcgct----catgctttctaa---taaagattgtttaaacttagtagttttggtttgcgttat---gtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCCAGATCAATAGGCGACACGGATGTGGGAGAATTTATTGTGCCAATACCACATGTAAAGC

upper sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 4

----gtagtgctcactgctcagtcattttgatgaagaaggattctaggatacaatatgagctctatgctttggaaacatttctgcatgggattttttaattaatttctcccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC
        |  |   ||| ||  ||  |  | |  ||| ||   |   ||  | |||     |  ||  ||| |      ||| ||||||     | ||   || | |    ||| ||||| || || ||||| |||||||| |||||||| || || || ||||||||||| || || ||||| || || |||||||| || || |||||||| ||||
gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattat---tcccttgtcttgaa------tcttcatggg-----tcaa---atgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC

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|71314548|gb|DR793896.1|DR793896

EST:     CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAG                         GTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATT
genomic: CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAGgtagtgctca ... ccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATT

EST: gi|19822432|gb|BQ048456.1|BQ048456

EST:     CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAG                         GTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATT
genomic: CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAGgtagtgctca ... ccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATT

EST: gi|31354352|gb|CD438709.1|CD438709

EST:     CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAG                         GTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATT
genomic: CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAGgtagtgctca ... ccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATT

EST: gi|71331543|gb|DR802616.1|DR802616

EST:     CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAG                         GTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTTCA-GGTCAAT
genomic: CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAGgtagtgctca ... ccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTT-CAAGGTCAAT

EST: gi|149079564|gb|EE168552.2|EE168552

EST:     CAGCGAGTGGAGGAGAAGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAG                         GTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCCAGGTCAATT
genomic: CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAGgtagtgctca ... ccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATT

EST: gi|94472234|gb|EB701192.1|EB701192

EST:     CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAG                         GTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGGTCA-T
genomic: CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAGgtagtgctca ... ccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGG-TCAAT

EST: gi|149045413|gb|EE047836.2|EE047836

EST:     CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAG                         GTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAGGGTCA-TT
genomic: CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAGgtagtgctca ... ccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATT

EST: gi|74233458|gb|DT641372.1|DT641372

EST:     CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAG                         GTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATT
genomic: CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAGgtagtgctca ... ccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATT

EST: gi|149108127|gb|EE292476.2|EE292476

EST:     CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAG                         GTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGC
genomic: CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAGgtagtgctca ... ccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGC

EST: gi|26455794|gb|CA827377.1|CA827377

EST:     CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAG                         GTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATT
genomic: CAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAGgtagtgctca ... ccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATT

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: 213

GACTGTGGATCACCGGCTAGAGGAGAATGCAGAGGAGCGTGAGCGCGTCACAGCGAGTGGAGGAGAGGTCAGCCGGCTTAATCTCTGTGGTGGACAGGAGgtagtgctca ... ccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC

Block sizes: 39 (upstream exon), 44 (downstream exon)
Score: 44

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 46

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 80

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atgctttggaaacatttctgcatgggattttttaattaatttctcccttttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC