ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...ttactagatatttcagccatatagaaaccagtgaaggacacatgctgagaagttaagatacattatttcatcattgaaaacagtgaatttctgtttgcagGTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGAC

Basic information

species	Zea mays
transcript	GRMZM2G460078_T02
intron #	12
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G460078_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g55590.1 (Oryza sativa), 3'ss of exon 12

ttactaga-tatttcagccatatagaaaccag-tgaaggacacatgctgagaagttaagatacattatttcatcattgaaaacagtgaatttctgtttgcagGTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGAC
|||  ||| | |   | |||   || |||||  ||||||   |||| ||||||   ||  | | || |||| |  || |  ||||| ||||| | || |||||| || |||||||| || |||||||| || ||||||||||| |||||||||||||||||||| || |||||||| ||||||||||| || |
ttagcagaatttgctaaccactaaggaaccaaatgaagggtgcatgttgagaatcaaatgt-ctttgtttcgttgttcagcacagttaatttgtatt-gcagGTTACTGCAGAATCATTTATTGATGGTGGGTTCTTCAAGACTGGTGATACAGTAACTGTAGACGATGAAGGATATTTCATAATTTTAGGGC

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|37385309|gb|CF629791.1|CF629791

EST:     TCTGCATTAGAAGTCCATCTCTTTTCAAGGAGTATTGGAAAAGACCAGAG                         GTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGTTACA
genomic: TCTGCATTAGAAGTCCATCTCTTTTCAAGGAGTATTGGAAAAGACCAGAGgtatgatcgt ... ctgtttgcagGTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACA

EST: gi|93012881|gb|EB638401.1|EB638401

EST:     ATTAGAAGTCCATCTCTTTTCAAGGAGTATTGGAAAAGACCAGAG                         GTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACA
genomic: ATTAGAAGTCCATCTCTTTTCAAGGAGTATTGGAAAAGACCAGAGgtatgatcgt ... ctgtttgcagGTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACA

EST: gi|78120378|gb|DV538762.1|DV538762

EST:     TCTGCATTAGAAGTCCATCTCTTTTCAAGGAGTATTGGAAAAGACCAGAG                         GTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACA
genomic: TCTGCATTAGAAGTCCATCTCTTTTCAAGGAGTATTGGAAAAGACCAGAGgtatgatcgt ... ctgtttgcagGTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACA

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), 48 (downstream exon)
Score: 81

CAAGATCATTATGGAGGACGGGGCTGAAACTACAACTGGAGTTGGCGAGCTCTGCATTAGAAGTCCATCTCTTTTCAAGGAGTATTGGAAAAGACCAGAGgtatgatcgt ... ctgtttgcagGTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGAC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 141

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 73

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 547

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgagaagttaagatacattatttcatcattgaaaacagtgaatttctgtttgcagGTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGAC