ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCAGCCAAAAGGTTTTGCTTATGTTGAATTTCTGGAACAAGAAGCTGTCCAGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaatatttggcagaggctcaatgcttttgcaagagattttaaagaaatctcaacagcgcttttacttctgctctacctttttgctctgtgctccacag

Basic information

species	Zea mays
transcript	GRMZM2G108919_T03
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G108919_T06 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g52140.2 (Oryza sativa), 5'ss of exon 4

GCAGCCAAAAGGTTTTGCTTATGTTGAATTTCTGGAACAAGAAGCTGTCCAGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaatatttggcagaggctcaatgcttttgcaagagattttaaagaaatctcaaca-gcgcttttacttctgc--tctacc---tttttgctctgtgctccacag
 ||||||||||||||||||||||| |||||||||||||||||||| || ||||| |||||||| ||||||||||| ||| |||||||||| ||||| ||||| |||||||      ||||  |    |   |   |   ||  || ||| |   ||   ||   | ||||      ||  | |||    ||| || | ||||||| ||||
ACAGCCAAAAGGTTTTGCTTATGTGGAATTTCTGGAACAAGAAGCAGTTCAGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaattaccaacagatccctgttttgtcacctgaaggattcaaaaactccttttcacatgtttttgtcctcgcaatttactcaatttctgttttgtgctcaacag

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|211527900|gb|FL308285.1|FL308285

EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC

EST: gi|9731847|gb|BE510599.1|BE510599

EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC

EST: gi|9731934|gb|BE510686.1|BE510686

EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAATTAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC

EST: gi|6563947|gb|AW231569.1|AW231569

EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCCCCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC

EST: gi|7135303|gb|AW498018.1|AW498018

EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC

EST: gi|211270122|gb|FL340668.1|FL340668

EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACT
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACT

EST: gi|50329632|gb|CO524758.1|CO524758

EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGCCAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCCCCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC

EST: gi|211177618|gb|FL479926.1|FL479926

EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC

EST: gi|60399607|gb|DN232418.1|DN232418

EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC

EST: gi|60351908|gb|DN218881.1|DN218881

EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC

EST: gi|89247954|gb|DY619740.1|DY619740

EST:     AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAG                         GTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC
genomic: AGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGC

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), 47 (downstream exon)
Score: 132

GCAGCCAAAAGGTTTTGCTTATGTTGAATTTCTGGAACAAGAAGCTGTCCAGGAAGCTCTGAACTTGAATGAATCGGAATTGCATGGTCGACAGATTAAGgttcagaaat ... tgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGCGGGTATAATCCCTACCATGGCTACCCTTATAGATCATATGGAGCACCGT

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 93

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 132