ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gttagtaatgaacttacacttcaaatttggttatgtggttatacctcctagatagttgataatgatgtcagtaacaaagtttactgtttttaatgtaatagGGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAA

Basic information

species	Zea mays
transcript	GRMZM2G157462_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g13820.2 (Oryza sativa), 3'ss of exon 8

gttagtaatgaacttacacttcaaatttggttatgtggttatacct-cctagatagttgataatgatgtcagtaacaaagtttactgtttttaatgtaatagGGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAA
|||||||| || ||| ||   | | || | || |    | |||||| |||| |  |   | |   ||  || ||||||  | |||||| ||  ||  ||||||| ||||| |||||| ||||||||||||||||||| || || ||||| |||||||||||||| ||  ||||| | || || || |||| ||| || ||||
gttagtaaagagctt-caaacctacttagatttta--atcataccttcctaaactgcaca-agcaattacaataacaa--tatactgtcttgtata-aatagGGGTCTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGGAAATTCCCAGAGAGAATTAAACAGCTGCCACTGGACAGGCACTTTGACCTCAGCAATGTTAAAA

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 8

gttagtaatgaacttacacttcaaatttggttat-gtggttatacctcc-tagatagttgataatgatgtcagtaacaaagttta-ctgtttttaatgtaat--agGGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAA
      || |   ||  | | ||  | |||| || |||    | | |     ||  |    |   ||| || ||||  |  |||  ||  |   ||| |  |  |||||  ||| |||||| |||||||||||||||||||||| || ||  |  | || ||| |||| ||||||||  ||||||| ||  | ||||| |||||||
------aaggtttttgaattgcatgtctggtgattgtgcccgttcatgtgctgaaggcctttttggatttcggtaaatatttttctctaataaaaatttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAA

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 8

-gttagtaatgaacttacacttcaaatttggttatgtggttatacctcctag-atagttgataatgatgtcagtaacaaagtttactgtttttaatgtaat----agGGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAA
   ||| | ||| ||   |  ||||  |||  |      ||| || |   |  | | |   |  |  || |  | |  |    | ||||  | ||| |  |    ||||    || |||||| |||||||||||||||||||||| || ||  |||| || || |||||||| || ||   |||||| ||| | ||||| |||||||
ttctagcattga-ctgcta--tcaaccttg--tgcaccattagacattacaacagaatctgttctactgcccattattag--ctgctgtcataaattttctttgcagGGTAGCGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAACAGGATCAAGCAGCTACCTTTAGATAAACATTTTGATATAAACAATGTCAAAA

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|9254689|gb|BE345157.1|BE345157

EST:     TGTGCCGAGAATTTGAGGACAAGTTTCTTGCTCACATAACATCTGGTGAG                         GGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGA
genomic: TGTGCCGAGAATTTGAGGACAAGTTTCTTGCTCACATAACATCTGGTGAGgttagtaatg ... aatgtaatagGGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGA

EST: gi|87155357|gb|DY400146.1|DY400146

EST:     TGTGCCGAGAATTTGAGGACAAGTTTCTTGCTCACATAACATCTGGTGAG                         GGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGA
genomic: TGTGCCGAGAATTTGAGGACAAGTTTCTTGCTCACATAACATCTGGTGAGgttagtaatg ... aatgtaatagGGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGA

EST: gi|30306992|gb|CD001665.1|CD001665

EST:     TGTGCCGAGAATTTGAGGACAAGTTTCTTGCTCACATAACATCTGGTGAG                         GGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGA
genomic: TGTGCCGAGAATTTGAGGACAAGTTTCTTGCTCACATAACATCTGGTGAGgttagtaatg ... aatgtaatagGGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGA

EST: gi|22472855|gb|BU037335.1|BU037335

EST:     TGTGCCGAGAATTTGAGGACAAGTTTCTTGCTCACATAACATCTGGTGAG                         GGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGA
genomic: TGTGCCGAGAATTTGAGGACAAGTTTCTTGCTCACATAACATCTGGTGAGgttagtaatg ... aatgtaatagGGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGA

EST: gi|31361304|gb|CD445661.1|CD445661

EST:     GTTTCTTGCTCACATAACATCTGGTGAG                         GGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGA
genomic: GTTTCTTGCTCACATAACATCTGGTGAGgttagtaatg ... aatgtaatagGGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGA

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: 343

AGAATCTATGGTACAAAGTGCCGAAGGAACCCGAGCAGTTGCTTTGGAGCTGTGCCGAGAATTTGAGGACAAGTTTCTTGCTCACATAACATCTGGTGAGgttagtaatg ... aatgtaatagGGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 360

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 332

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 229

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cctagatagttgataatgatgtcagtaacaaagtttactgtttttaatgtaatagGGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAA