ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaacatatagttgttgatagatgtgtacgtggataggcttactagtttgcctaacttatgcgctttcttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAATCATATTCAGAAACCATAAGTACTTTAAAATTTGCTGAAAGGGTTTCTGG

Basic information

species	Oryza sativa
transcript	LOC_Os01g54080.1
intron #	17
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 8

---------------------------gtaacatatagttgttgatagatg-tgtacgtggataggcttactagtttgcctaa--cttatgcgctttcttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAATCATATTCAGAAACCATAAGTACTTTAAAATTTGCTGAAAGGGTTTCTGG
                           | || |    |      |||| || | ||  |     | | || || ||    |||  ||  |  | |||| || |||||| |||||||||||||| |||||||||||||| || || |||| || ||||||||||||||| ||||| ||||| || ||||||||||||||||||||
gtaacaataacatatagttgttcctcggaaaaaaggggcaccaaatagttggtttatatatgcggacatattatttatgataattctcgtctgttttcatgcagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G323622_T01 (Zea mays), 3'ss of exon 8

--------------------------gtaacatatagttgttgatagatgtgtacgtggatag-gcttactagtttgcctaa--cttatgcgctttcttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAATCATATTCAGAAACCATAAGTACTTTAAAATTTGCTGAAAGGGTTTCTGG
                          |  || |  | | |||  |  || | | |    |||   ||||  ||||    |||  ||  |  | ||||||| ||| ||||||||||||||| | |||||||||||||| || || |||| |||||||||||||||||| ||||| ||||| || ||||||||||||||||||||
gtaacatatagttgttcctcaaaaaagggacgtcaaatagttagtttatatatgcagacatattacttatgagttatgataattctcttctgttttcttgcagGCGGACAAGCAAAGACATTGATGTTTGTTCAAATTAATCCGGATACTGAATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA05G35130.1 (Glycine max), 3'ss of exon 15

---------------------gtaacat-atagttgttgatagatgtgtacgtggataggcttactagtttg----cctaacttatgcgctttcttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAATCATATTCAGAAACCATAAGTACTTTAAAATTTGCTGAAAGGGTTTCTGG
                     || |  | | |    ||||    | | || || |||   ||||  |  ||     | |  |||      | |     |||||  ||||| |||||||| |||||||||||||| ||  | ||  |    |||||||| |||||  | || |||||||| ||||||||||||||||||||
gtaaatctttattcatcatttgttatgtcacatgccttgaatcttttctatgtagattttcttatgatctttgactcttgtctttgattttattgcacagGTGACCAAGCGAAGACACTCATGTTTGTTCAAATTAATTCAGACGTAAGTTCATATTCTGAAACACTGAGCACTTTAAAGTTTGCTGAAAGGGTTTCTGG

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA13G33390.1 (Glycine max), 3'ss of exon 13

----------------------------------------------------------------------------------------------------------------gtaacatatagttgttgatag-atgtgtacgtggataggcttactagtttgcctaacttatgcgctttcttgta--gGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAATCATATTCAGAAACCATAAGTACTTTAAAATTTGCTGAAAGGGTTTCTGG
                                                                                                                   || | || |   |   |  || | |   | |||| | || | | ||     |  |  |    ||| ||| |  ||||| || || |||||||| ||||| || ||||| ||  | ||| |  | || | ||| ||| |  ||||||||||||| |||||||| |||||||||||
gtaaaatcatagtttatcatttcttaccttgccttgctagtatctaacacttcatgtcttgccttgctagtatgcacaaaagtgaaaaatccttgagtttctttatgtcttttggacttgtattctataccactatttctgattagataagatt-ccatttgaaacatatgtttaattttattgcacagGTGGTCAGGCCAAGACACTCATGTTAGTCCAAATTAATTCAGATTTAAAGTCTTTTTCTGAATCTCTAAGTACTTTAAAGTTTGCTGAGAGGGTTTCTGG

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 17
lower sequence: AT1G73860.1 (Arabidopsis thaliana), 3'ss of exon 16

----gtaacatatagttgttgatagatgtgtacgtggataggc----ttactagtttgcctaacttatgcgctttcttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAATCATATTCAGAAACCATAAGTACTTTAAAATTTGCTGAAAGGGTTTCTGG
    || |  | ||  | | ||||      | | || ||| |     | |  | |||   |    | ||   |  ||| |||| |||| ||||||||||||||||||||| ||| | ||||||||   |   ||||| |||||  | || ||||| || |||||||| ||  | || |||||
gttagtgaactttatatat-gataaccacattcatgaataagaaatatcataacttttgtttctatgtgatgtggcttatagGAGGACGAGCAAAGACACTAATGTTTGTGCAACTCAACCCTGACGCTACTTCATACTCAGAGTCAATGAGTACCTTGAAATTTGCAGAGCGTGTCTCTGG

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 17
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 3'ss of exon 16

------gtaacatatagttgttgatagatgtgtacgtggat-aggcttactagtttgcctaacttatgcgctttc---ttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAATCATATTCAGAAACCATAAGTACTTTAAAATTTGCTGAAAGGGTTTCTGG
         | || |  |  |   |   |     ||||    |   || |||  ||  ||    | || | |||    |   |||||| | ||||||||||||||||||||||||| | || |||||||||   |||||||||||  | || |||||||| ||||| || ||  | || |||||
gttaactccaaatcttctgctctgttttttcaatcgtgatcgaaattttctaacttatct---ctgtgtgatttaacatcacagGTGGTCGAGCAAAGACACTAATGTTTGTTCAACTGAATCCTGATATTACTTCATATTCAGAGTCAATGAGTACTTTGAAATTCGCAGAGCGTGTCTCTGG

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 3'ss of exon 17

-------------------------------------------------------------------------gtaacata--tagttgttgatagatgtgtacgtgga-taggcttactagtttgcctaacttatgcgctttc--ttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAATCATATTCAGAAACCATAAGTACTTTAAAATTTGCTGAAAGGGTTTCTGG
                                                                          | |  |   ||| |    ||||   | |   || | |     ||   | ||   ||  || | |  | |    |  |||||| ||||||||||| || |||||||| ||  | || |||||| |  | |||| ||| |||||   ||||||||| ||||||||||| |||||||||||
gtacttcactgttttccagttgcttttagcaataaatcccttcacctgtcttattgtttcgtcaggactctaaattatttccttagctcccaatagtcctctttttgaacttcatatagcggatt-tttattttctactttataaactacagGTGGTCAAGCAAAGACTCTTATGTTTGTGCAGCTTAATCCTGATGTGAATTCATTTTCTGAAACTGCAAGTACTTTGAAATTTGCTGAGAGGGTTTCTGG

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|58682559|gb|CK071246.1|CK071246

EST:     TGTGCCATATAGAAACAGCAAGCTAACTCAAGTTCTTCAGAGTTCTTTAG                         GTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATGTTGAAT
genomic: TGTGCCATATAGAAACAGCAAGCTAACTCAAGTTCTTCAGAGTTCTTTAGgtaacatata ... tttcttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAAT

EST: gi|58595522|gb|CK006050.1|CK006050

EST:     TGTGCCATATAGAAACAGCAAGCTAACTCAAGTTCTTCAGAGTTCTTTAG                         GTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATGTTGAAT
genomic: TGTGCCATATAGAAACAGCAAGCTAACTCAAGTTCTTCAGAGTTCTTTAGgtaacatata ... tttcttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAAT

EST: gi|163928538|gb|EG710859.1|EG710859

EST:     TGTGCCATATAGAAACAGCAAGCTAACTCAAGTTCTTCAGAGTTCTTTAG                         GTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAAT
genomic: TGTGCCATATAGAAACAGCAAGCTAACTCAAGTTCTTCAGAGTTCTTTAGgtaacatata ... tttcttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAAT

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: 47 (upstream exon), 61 (downstream exon)
Score: 16

CTCTCTGCTCTTGGAGATGTCATTTTTTCTTTGGCCCAGAAGAATGCCCATGTGCCATATAGAAACAGCAAGCTAACTCAAGTTCTTCAGAGTTCTTTAGgtaacatata ... tttcttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAATCATATTCAGAAACCATAAGTACTTTAAAATTTGCTGAAAGGGTTTCTGG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agatgtgtacgtggataggcttactagtttgcctaacttatgcgctttcttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAATCATATTCAGAAACCATAAGTACTTTAAAATTTGCTGAAAGGGTTTCTGG