ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

Basic information

species	Oryza sativa
transcript	LOC_Os01g17170.2
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G043109_T01 (Zea mays), 3'ss of exon 2

gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                                       | |      |   ||   | || ||  |   | | |||||     ||     |           || |||||| |||||   |     ||||||   ||||  ||||| ||||||||||| |||||||| ||||||||||| |||||||| |||||| | |||||||||||||||||||||||||||||||||||||||||||||
-------------------------------------------------------------------------------------catgcatgttttcctgattgtgttcaatttgaggctctagggtaatgatgagggcatgg-------agaaattcagctgaaagtttcatgtgatttgcactgtgtagGTTTTTGAACAAGGGTCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTCACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2

gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgct----gttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                                                             || ||  |    |||     ||  |||  |  || | | |  || |||||| |||||   |     ||||||   ||    ||| |||||||||||||||||||||||||| ||||||||||| |||||||| |||||| |||||||||||||||||||||||||||||||||||||||||||||||
------------------------------------------------------------------------------------------------------------gtacgcacctacctta-----tctcttttcatccattcggg-gagaaattcagctgaaagtttcatgtgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 2

gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagc-ttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctg-catgattt--atgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                                                ||  ||||    ||  || || | ||||      ||| | |    |    | | |    |  |    || | ||  || | | ||||  || |||| |||||| |||||||||||  | ||||||||||| ||||| |||||| | || ||||||||||| ||||| || ||||| || |||||||| ||||| ||||||
-----------------------------------------------------------------------------------------------gtatggaaacgccttgtgcctttaatttttaattatccttctttgattttct-atttgatatcttgtttgtagtgcatgacctcattttgattctgtgcagGTTTTTGAACAAGGGTTTATCTGATTTCAATTTGGCTCTGGACTTGGGTTTCTTGACCAAAGCTAGAAAATACACATTTTTCAAGCCAAAGTTTATCTTC

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G30350.1 (Glycine max), 3'ss of exon 2

gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgattt--atgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                              || ||         || ||  |    ||  ||||   ||| | ||       | |||| |  ||  | |  | |    ||    || || | || ||| ||||  || |||| |||||| |||||||| ||  | |||||||| || ||||| |||||| | || ||||||||||| ||||| || ||||| || |||||||||||||| ||||||
----------------------------------------------------------------------------gtatggacacaccttgtgccttta----attcttaattctcattctttcatttcctatttgatatc--tcgtttgaatgtttgttgtgtatggcct-cattattttgattctgtgcagGTTTTTGAACAAAGGTTTATCTGATTTTAATTTGGCTCTGGACTTGGGTTTCTTGACCAAAGCTAGAAAATACACATTTTTCAAGCCCAAGTTTATCTTC

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 3

gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                                                       || || |   ||| |   | ||| | ||  |||  | ||       ||||   ||||| |    ||     || |  | |  |   ||||||||||||||||||  ||||||||||||||||||| || ||  | || ||| |||| ||||| ||||| ||||| ||||||||||| || |||||||||
-----------------------------------------------------------------------------------------------------gtaagatct---cttaacactaaggacctctctttttaatc-------taagtgtttcaattttgatg-----ataaactttttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTTCCTGACAAAGGCAAGGAAATACACTTTCTTCAAGCCAAAATTCATCTTC

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 3'ss of exon 2

gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgctgtt-cagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                       |   | ||||     |  |   |  || |    |||||   | |  || | |||   | |  | || |  |||  | ||| | | | |      ||| |   |  || | | |  | |   |   |||   || ||||  || ||||||| ||| ||  ||||||| ||  | ||||||||||| |||||  ||||| | |||||| | || |||||||| ||||||||||| || ||||||||||||||||||
-------------------------------------gtatgcaaacaactctctgcccttctcccttcctcactcatggtcatatgcatcatagtttgc-agaacaagtaa--tacagctgttgag------ttttatagcttttaactgaaaagtctga---aataaacttcatg--ttctgctgttgcagATTTCTGAACAAAGGTTTATCTGATTTCAATTTGGCTTTGGACTTGGGGTTCCTCACAAAGGCTAGAAAGTACACCTTTTTTAAGCCCAAGTTCATCTTC

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ28505 (Selaginella moellendorffii), 3'ss of exon 2

gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC--------------------------------------------------------------
                                                                   ||   | | |   | | ||| |  |  |  |  ||  || |   |                                                                                                      || || |||||||| ||||| || || ||  ||||||| ||  ||||||||||||||||||||||  |||||||||||                                                              
------------------------------------------------------------------gttctcagtta--ctcagctggaaaaaaagcatcgatcatttcctatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgactttaacttggctctggatcttggatttctgaccaaagCCCGGAAGTACACCTTCTTCAAGCCACAGTTCATCTTCTACGCGACGTATCTCTCGGAGAAGATCGGCTACTGGAGGTACATTACTATCTACAGGCACTT

upper sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ30397 (Selaginella moellendorffii), 3'ss of exon 2

gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaat-tcaactgaattgtctgcatgatttatgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                                                                          || |   ||  ||||   ||| |||   ||  |   || |    |||  ||  ||| || ||       |||||| ||||||| ||  | || || || |||||||| ||||| || || ||  ||||||| ||  ||||||||||||||||||||||  |||||||||||
-------------------------------------------------------------------------------------------------------------------------gtaagttctcagtttc---tcagttggaaaaaaagcatcgatc--atttcctatatg-ttcat-------agGTTCCTGAACAAAGGATTATCCGACTTTAACTTGGCTCTGGATCTTGGATTTCTGACCAAAGCCCGGAAGTACACCTTCTTCAAGCCACAGTTCATCTTC

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|29662324|gb|CB658599.1|CB658599

EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT

EST: gi|29672478|gb|CB668753.1|CB668753

EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT

EST: gi|38474941|gb|CF959074.1|CF959074

EST:     GTGGCTGAGATCTACTCGCTCATGTCCANGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTAGATTTCAACTTGGCACTGGACCTCGGGT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCT-GATTTCAACTTGGCACTGGACCTCGGGT

EST: gi|29676338|gb|CB672613.1|CB672613

EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT

EST: gi|38471854|gb|CF955985.1|CF955985

EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT

EST: gi|38473793|gb|CF957925.1|CF957925

EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT

EST: gi|29619025|gb|CB624037.1|CB624037

EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT

EST: gi|38474054|gb|CF958186.1|CF958186

EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT

EST: gi|29663604|gb|CB659879.1|CB659879

EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT

EST: gi|2801122|gb|AA754416.1|AA754416

EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT

EST: gi|29620880|gb|CB625891.1|CB625891

EST:     GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG                         GTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT
genomic: GTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTT

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: 69 (upstream exon), 73 (downstream exon)
Score: 187

AAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGGgtaagtagta ... tgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aactcaattgagtaagcaattcaactgaattgtctgcatgatttatgctgttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC