ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gttagcaatatgaacactggtttgcactttaattattgaaaacagcataaatccagtcaatgatatttcttctatcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGACCGACCATTTGTAAAG

Basic information

species	Oryza sativa
transcript	LOC_Os03g05200.1
intron #	16
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os03g05200.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G107651_T01 (Zea mays), 3'ss of exon 13

gttagcaatatgaacactggtttgcact-ttaattattga-------------------aaacagcataaa-tccagtcaa-tgatatttcttctatcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGACCGACCATTTGTAAAG
|||||||||| ||||| || | |  ||  ||||| |||                     | ||| | |||| |||| |  | | || ||    ||   | |||||||||| |||||||| ||||||||||| || ||||| ||||||||||| ||  |||||||| |||||
gttagcaatacgaacattgttctctacccttaataattatgttctttgttagttcacttagacatcgtaaaatccatttgagtaatgttagccctgaatgatcagGTTTCTTTGCTTCTGAAAGACAGTTTCATTGATTCGTTCCCCTCAAATGATAGACCATTTATAAAG

upper sequence: LOC_Os03g05200.2 (Oryza sativa), 3'ss of exon 15
lower sequence: AT2G20320.1 (Arabidopsis thaliana), 3'ss of exon 17

---gttagcaatatgaacactggtttgcactttaattattgaaaacagcat----aaatccagtcaatgatatttcttctatcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGACCGACCATTTGTAAAG
    |||   ||||    |||    |  |   | |  |   |  ||   ||    |  ||    |||   | |   |  |   ||||||||||||  | |||||||| |||||||||||||||||||| ||    |  || ||||| ||  | |||
gtacttacttatatagctactctcctcgaagctgaacaagaactactttatttctatctctcaccaactctctaaatctttctttatcagGTTTCTCTACTTCTAAAGGACAGTTTTATCGATTCATTTCCTGGTAGAGATCGACCCTTCATTAAG

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|38477933|gb|CF962066.1|CF962066

EST:     CTGACCTGCGATCTCATACCATCACCAATGTACAGTCAAATAATGACAGG                         GGTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGAC
genomic: CTGACCTGCCATCTCATACCATCACCAATGTACAGTCAAATAATGACAGGgttagcaata ... atcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGAC

EST: gi|29614852|gb|CB619865.1|CB619865

EST:     CTGACCTGCGATCTCATACCATCACCAATGTACAGTCAAATAATGACAGG                         GTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGAC
genomic: CTGACCTGCCATCTCATACCATCACCAATGTACAGTCAAATAATGACAGGgttagcaata ... atcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGAC

EST: gi|25807379|gb|CA763340.1|CA763340

EST:     CTGACCTGCGATCTCATACCATCACCAATGTACAGTCAAATAATGACAGG                         GTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGAC
genomic: CTGACCTGCCATCTCATACCATCACCAATGTACAGTCAAATAATGACAGGgttagcaata ... atcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGAC

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 1 RNA-Seqlibrary.

Block sizes: 52 (upstream exon), 64 (downstream exon)
Score: 8

AGCTTGGCAGTTCTTGAACGTCATGAGATCCTATCTGGAGTCGCTTTGTTCTGACCTGCCATCTCATACCATCACCAATGTACAGTCAAATAATGACAGGgttagcaata ... atcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGACCGACCATTTGTAAAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttaattattgaaaacagcataaatccagtcaatgatatttcttctatcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGACCGACCATTTGTAAAG