ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gttagactatatttatgcctccaaaaaaactcactttacatttttgtcatgtttctaatctatatttttttaatcagGTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTTTTGAGATACCACTCGATGTTGTAGGACAACCATTAGAAAAGCTACTTTC

Basic information

species	Oryza sativa
transcript	LOC_Os04g33060.1
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os04g33060.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G069708_T01 (Zea mays), 3'ss of exon 6

-----------gttagactatat----ttatgcctc-caaaaaaactcactttacatttttgtcatgtttctaatctatatttttttaat--cagGTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTTTTGAGATACCACTCGATGTTGTAGGACAACCATTAGAAAAGCTACTTTC
            | | || || |    | | |  || |     |||||| | ||  |  ||||||| |  |  | ||   ||||||   |  ||||||| ||  ||||||| || |||||||| ||||||||||||||| |||| || ||| |||||||||| | ||| ||||||||||| || ||| | || ||
gttagaaatacttcacaccatttgttgtcaggtttctctctcgaactcaatgta--tccttgtcatataccggacctgccttttttcttttacagGTGTCGTGTTGAGGCCAGGCTTCATTTACGGTAAAAGGAAAGTAAATGGCTTCGAGGTACCACTCGACGCTGTCGGACAACCATTGGAGAAGTTGCTCTC

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|86497486|gb|CI140119.1|CI140119

EST:     TGGTAAGAGAAAGGCTGAATCTGAAGTCCTCTCCAAATACCCAACCTCAG                         GTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTT
genomic: TGGTAAGAGAAAGGCTGAATCTGAAGTCCTCTCCAAATACCCAACCTCAGgttagactat ... ttttaatcagGTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTT

EST: gi|29657208|gb|CB653483.1|CB653483

EST:     TGGTAAGAGAAAGGCTGAATCTGAAGTCCTCTCCAAATACCCAACCTCAG                         GTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTT
genomic: TGGTAAGAGAAAGGCTGAATCTGAAGTCCTCTCCAAATACCCAACCTCAGgttagactat ... ttttaatcagGTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTT

EST: gi|88527778|gb|CI455961.1|CI455961

EST:     TCCTCTCCAAATACCCAACCTCAGG                         GTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGT
genomic: TCCTCTCCAAATACCCAACCTCA-Ggttagactat ... ttttaatcagGTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGT

EST: gi|86261557|gb|CI017299.1|CI017299

EST:     TGGTAAGAGAAAGGCTGAATCTGAAGTCCTCTCCAAATACCCAACCTCAG                         GTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTT
genomic: TGGTAAGAGAAAGGCTGAATCTGAAGTCCTCTCCAAATACCCAACCTCAGgttagactat ... ttttaatcagGTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTT

EST: gi|29687807|gb|CB684082.1|CB684082

EST:     TGGTAAGAGAAAGGCTGAATCTGAAGTCCTCTCCAAATACCCAACCTCAG                         GTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTT
genomic: TGGTAAGAGAAAGGCTGAATCTGAAGTCCTCTCCAAATACCCAACCTCAGgttagactat ... ttttaatcagGTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTT

EST: gi|89161982|gb|CI102330.1|CI102330

EST:     CAAATACCCAACCTCAG                         GTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTT
genomic: CAAATACCCAACCTCAGgttagactat ... ttttaatcagGTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTT

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: 50 (upstream exon), 75 (downstream exon)
Score: 43

GTTCATGATTACAATCTTCCATCCTTTCTTCTTAACTCGGGTTACTTCACTGGTAAGAGAAAGGCTGAATCTGAAGTCCTCTCCAAATACCCAACCTCAGgttagactat ... ttttaatcagGTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTTTTGAGATACCACTCGATGTTGTAGGACAACCATTAGAAAAGCTACTTTC

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaactcactttacatttttgtcatgtttctaatctatatttttttaatcagGTGTTGTACTGAGGCCTGGTTTCATTTATGGTAAAAGGAAAGTAGATGGTTTTGAGATACCACTCGATGTTGTAGGACAACCATTAGAAAAGCTACTTTC