ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgtgcgcttctacaagccccgtcccgatcacagctgtgaatacttcggttactgaactgtttttttctctcgatctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCTTCAACTTCCCGGAGGGTGGTGTTGAGCTCTACGCAGAGAAGGTGAACAA

Basic information

species	Zea mays
transcript	GRMZM2G093902_T02
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G093902_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 2

------------gtatgtg-cgcttcta---caagccccgtcccgatcacagctgtgaat-acttcggttac-tgaactgtttttttctctcgatctcgctt-agGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCTTCAACTTCCCGGAGGGTGGTGTTGAGCTCTACGCAGAGAAGGTGAACAA
            ||  ||| |  ||||       ||  ||   ||||  |   || || | |   ||| | |  || ||| |  |||   |  ||     || ||||||||||||  |||||||| | |||||||| || ||||| |||||||| |||||||||||||||  ||| || ||||||||||| ||||||||||||||
gtgagttcgtgagttcgtggcatttctgatctgggcagcgaggcgattccg--tgcgatttatcccgggtgcgcgatctgatgctttggatgaatgcgatttcagGCGAGAAGGGGAGGAGGATCCGCGAGCTGACGTCCGTGGTGCAGAAGCGGTTCAACTTCCCGGAGAATGGCGTCGAGCTCTACGCCGAGAAGGTGAACAA

upper sequence: GRMZM2G093902_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g41750.3 (Oryza sativa), 3'ss of exon 1

gtatgtgcgcttctacaagccccgtcccgatcacagctgtgaatacttcggttactgaactgtttttttctctcgatctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCTTCAACTTCCCGGAGGGTGGTGTTGAGCTCTACGCAGAGAAGGTGAACAA
|    |   ||||    ||    |   ||| | |  |   ||  |  |     || |      | |   |  |||  |  ||  || ||    |  |   | | ||   |   || | ||   |  |||||||                                                     
gcggttcaacttcccggagaatggcgtcgagctctacgccgagaaggtgaacaaccgcggc-ctctgcgccatcgcccaggccgagtcgctccg--ctacaagCTCCTCGG--TGGCCTCGCCG--TCAGAAG-----------------------------------------------------

upper sequence: GRMZM2G093902_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0008g01750.t01 (Vitis vinifera), 3'ss of exon 2

---------gtatgtgcgcttctacaa------gccccgtcccgatcacagctgtgaatacttcggttactgaactgtttttttctctcgatctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCTTCAACTTCCCGGAGGGTGGTGTTGAGCTCTACGCAGAGAAGGTGAACAA
         || | |  || |  |  |      |   | | | | | ||    | |  |  || | | | ||   || |||||| | |   | |   | ||| || |||||    |||||||||||||||||||| |||||||||||| | || || || || ||     |||| ||||| || || ||||| || |||||
ttgtcacttgtttctcggcattgaagaaatgtggtttcatgctgttaaccatagggttttattggttgaatgggttgattttttattttt-tatttttcagGTGAAAAGGGAAAAAGGATCAGGGAGCTGACTTCAGTGGTTCAGAAGAGGTTTAAATTTCCTGAAAACAGTGTGGAGCTTTATGCTGAGAAAGTTAACAA

upper sequence: GRMZM2G093902_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S127_74V6.1 (Physcomitrella patens), 3'ss of exon 2

---------------------------------------------gtatgtgcgcttctacaagccccgtccc---gatcacagctgtgaatacttcggttactgaactgtttttttctctc-gatctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCTTCAACTTCCCGGAGGGTGGTGTTGAGCTCTACGCAGAGAAGGTGAACAA
                                             || | || | |  |    |     || |   |  |  || ||    | |   |||    | | ||   |    |  | | || |   |||| |||||||| || ||||||||||| ||||| || ||||| |||||| | ||  | ||||||||||||  ||| ||| | ||||| ||||||||||||||
gtgagtctcttggctgcactgacattatgcgctatggatctggtagtctttgagataattagggttttttctctttggccggaggtgaatttgcgggggtagtcggattgaagtagggtgactgctccctggtagGTGAGAAGGGACGAAGGATCAGGGAACTGACCTCCGTGGTACAGAAGAGGTTTCAGTTCCCGGAGGGTACTGTGGAGTTGTACGCCGAGAAGGTGAACAA

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|211411263|gb|FK965131.1|FK965131

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|74240382|gb|DT648296.1|DT648296

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|148973769|gb|EE024903.2|EE024903

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|211413802|gb|FK965136.1|FK965136

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|211411267|gb|FK965135.1|FK965135

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGGAGCTGACTTCTGTGGTTCAGAAGCGC
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGG-AGCTGACTTCTGTGGTTCAGAAGCGC

EST: gi|211411264|gb|FK965132.1|FK965132

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|91052942|gb|EB163360.1|EB163360

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|60347103|gb|DN214076.1|DN214076

EST:     GAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: GAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|76013473|gb|DT940643.1|DT940643

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|211411261|gb|FK965129.1|FK965129

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|88757758|gb|DY541899.1|DY541899

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|78109693|gb|DV528109.1|DV528109

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|211053864|gb|FL037807.1|FL037807

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|60398401|gb|DN231217.1|DN231217

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|50339749|gb|CO534875.1|CO534875

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|60346506|gb|DN213479.1|DN213479

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|74244112|gb|DT652026.1|DT652026

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

EST: gi|78024902|gb|DV493289.1|DV493289

EST:     CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCG                         GCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT
genomic: CATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 220

CGCGAGCTCGCGGAGGATGGCTACTCCGGCGTCGAGGTCCGCGTCACCCCCATGCGCACCGAGATCATCATCCGTGCCACCCGCACTCAGAACGTTCTCGgtatgtgcgc ... tctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCTTCAACTTCCCGGAGGGTGGTGTTGAGCTCTACGCAGAGAAGGTGAACAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cacagctgtgaatacttcggttactgaactgtttttttctctcgatctcgcttagGCGAGAAGGGCCGGAGGATCAGGGAGCTGACTTCTGTGGTTCAGAAGCGCTTCAACTTCCCGGAGGGTGGTGTTGAGCTCTACGCAGAGAAGGTGAACAA