ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtattgttttttcatctgtcaggctgatttgtgcaatccaatatttgtttaatatgataatctgaatatttgtttaatattactgttctttcatcttatgctttcaaataatttgaattgtttgcaatttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCGGTGTACTTGGTTGCTGACTATGTCGAAGT

Basic information

species	Zea mays
transcript	GRMZM2G399073_T02
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 5

gtattgttttttc------atctgtcaggctgatttgtgcaatccaatatttgtttaatatgataatctgaatatttgtt----taatattactgt---tctttcatcttatgctttcaaataatttgaattgtttgcaatttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCGGTGTACTTGGTTGCTGACTATGTCGAAGT
|||||  |  ||       || | ||     | | |||| | ||   |  |       ||  || ||||   | |||||      ||| ||||       | || | ||||  |||   | | ||   ||||  ||| |||||||  ||||||||||| |||||||||||| |||| |||||||||||||| ||||| || || |||||||| ||||| || || |||||||||||||||||||| |||||
gtattactcctttgtactgatttctcttaaagttatgtgtattctcttgctaaaactttagtattatctatttgtttgtaaagagaattttaccaagtgccatttaacttaaactt--gagtgataccaattccttgaaattttt--gcagCTTTTGTGGAAAAGATGCAGACTGGGGGTGACCTCAATCTCATTGGGCAATTCGGTGTTGGTTTCTATTCAGTATACTTGGTTGCTGACTATGTTGAAGT

upper sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 5

gtattgttttttcatctgtcaggctgatttgtgcaatccaatatttgtttaatatg-ataatctgaatatttgtttaatattactgttctttcatcttatgctttcaaataatttgaattgtttgcaatttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCGGTGTACTTGGTTGCTGACTATGTCGAAGT
                                                    |||| ||  | ||     ||| | ||   || | ||   |  |  | || ||   ||  || | |||||   ||  | ||  | |||| ||||| || ||||||||  |  | || || |||||||| ||||| |||||||| || ||||||||||| || ||  | || |||||||||||||||| 
--------------------------------------------------ggtatgtatgttgtggcacattgctgaa--gtagtttttgcttgtaatgtggttgggaa-gatgttaattgga-gctgtgttaattcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTCGTGGCTGACTATGTCGAAG-

upper sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 5
lower sequence: EFJ28825 (Selaginella moellendorffii), 3'ss of exon 5

gtattgttttttcatctgtcaggctgatttgtgcaatccaatatttgtttaatatgataatctgaatatttgtttaatattactgttctttcatcttatgctttcaaataatttgaattgttt--gcaatttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCGGTGTACTTGGTTGCTGACTATGTCGAAGT
                                                                                    || ||||| |    | |||| || |   |||||    ||      || ||||| ||| ||| |||||||||||||||| ||||||||| | ||| | ||||| |||||||| || || |||||||||||||| ||||| || || || ||||| ||
------------------------------------------------------------------------------------gtgctttctttgactcctttgaattttgttgaacaactttgatgtttcttttgtagCATTTTTCGAAAAGATGCAGTCAGGAGGTGACTTAAATTTGATTGGCCAGTTTGGAGTCGGTTTCTACTCGGTGTATTTGGTCGCGGATTACGTCGAGGT

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|56538364|gb|CX054073.1|CX054073

EST:     GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTTAG                         CTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
genomic: GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgtttt ... ttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT

EST: gi|149004856|gb|EE039364.2|EE039364

EST:     GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAG                         CTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
genomic: GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgtttt ... ttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT

EST: gi|24767582|gb|CA402726.1|CA402726

EST:     GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAG                         CTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
genomic: GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgtttt ... ttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT

EST: gi|31360086|gb|CD444443.1|CD444443

EST:     GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAG                         CTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
genomic: GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgtttt ... ttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT

EST: gi|148965480|gb|EE016290.2|EE016290

EST:     GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAG                         CTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
genomic: GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgtttt ... ttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT

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: 319

AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgtttt ... ttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCGGTGTACTTGGTTGCTGACTATGTCGAAGT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 260

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 824

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgttctttcatcttatgctttcaaataatttgaattgtttgcaatttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCGGTGTACTTGGTTGCTGACTATGTCGAAGT