ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gcaattttttgtctccaatttatgtttgtttttaatttcattatataaattctttgaatactcatcttgcttggtgtatcatcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTTGGCTTTGCTTACATTGGTGCAAAAGCACCAGGAGGGGGTGCAGTTGGTA

Basic information

species	Zea mays
transcript	GRMZM2G047564_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G047564_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g39344.2 (Oryza sativa), 3'ss of exon 4

--------gcaattttt-tgtctccaatttatgttt-gtttttaatttcattatataaattctttgaat------actcatcttgcttg-gtgtatcatcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTTGGCTTTGCTTACATTGGTGCAAAAGCACCAGGAGGGGGTGCAGTTGGTA
        | ||||| | |  |||  |||||  |||  | || |   |   |||    | | |||||||       ||||   || | |  || |  |   || ||||| || ||||| || ||||| ||||||||||||||| ||||||| || ||||||||||||||||||||||| ||||| |||||||| ||||| ||||   
gcaagtttgaaatttctgtaactctgatttagattttatgttcatcatttgtattctcagtatttgaattgtaaggctcaaaatgttcgcatgcactactgttacagAGGACGCTCCTGGCTATGCCAGAAAATGGTATTGGCTTGTTCCCGGACGTTGGCTTTGCTTACATTGGTGCCAAAGCTCCAGGAGGTGGTGCTGTTG---

upper sequence: GRMZM2G047564_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv11s0016g04290.t01 (Vitis vinifera), 3'ss of exon 6

--gcaattttttgtctccaatttatgtttgtttt-taatttca-ttatataaattctttgaatactcatcttgcttggtgtatcatcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTTGGCTTTGCTTACATTGGTGCAAAAGCACCAGGAGGGGGTGCAGTTGGTA
    |||            |  ||  ||||||||  || |||| ||| |  |||  | | | | || || ||  || ||      |  || |||||||| || || |||||||| |||||||| |||||| |||| ||||||||||| ||||||||||| |  ||| |    |||||||  ||  ||||||   
gtataatggccatatatggacataaatttgttttgcaacttcaattagaataatgttctaatttctgatatttatttgtactaatttgtttcagAGAACTCTTCTTGCCATGCCAGAAAATGGAATTGGCTTGTTTCCAGATGTTGGATTTGCTTACATAGCAGCACAGAGTCCAGGAGAAGGATCAGTTG---

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|71312658|gb|DR792850.1|DR792850

EST:     GATTTGGAATTGGGCTATCAGGGCATGGCCGCTACCGCATTATTACAGAG                         AGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTT
genomic: GATTTGGAATTGGGCTATCAGGGCATGGCCGCTACCGCATTATTACAGAGgcaatttttt ... atcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTT

EST: gi|211063902|gb|FL196766.1|FL196766

EST:     GATTTGGAATTGGGCTATCAGGGCATGGCCGCTACCGCATTATTACAGAG                         AGAACACTCCTAGCCATGCCTGAAAATGGT
genomic: GATTTGGAATTGGGCTATCAGGGCATGGCCGCTACCGCATTATTACAGAGgcaatttttt ... atcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGT

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), 48 (downstream exon)
Score: 42

ACATGAGTATGCAAAACCTTATATATGCTTGATGGATGGAGTGACAATGGGATTTGGAATTGGGCTATCAGGGCATGGCCGCTACCGCATTATTACAGAGgcaatttttt ... atcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTTGGCTTTGCTTACATTGGTGCAAAAGCACCAGGAGGGGGTGCAGTTGGTA

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 160

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttcattatataaattctttgaatactcatcttgcttggtgtatcatcattgcagAGAACACTCCTAGCCATGCCTGAAAATGGTATTGGCCTGTTCCCAGATGTTGGCTTTGCTTACATTGGTGCAAAAGCACCAGGAGGGGGTGCAGTTGGTA