ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatttcttgctctgttccacagttcattttgcacacttgtgttattttctgaacttggattcatgatatttatgtattcaatcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG

Basic information

species	Oryza sativa
transcript	LOC_Os02g53140.1
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G126795_T01 (Zea mays), 3'ss of exon 9

gtatttcttgctctgttccacagttcattttgca-----cact--tgtgttattttctgaacttggattcatgatatttatgtattcaatcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
    |     |||| ||  |||||||||| ||||     || |  ||| ||||  |   ||||  |     || | ||| ||||||    | |  | ||||||||||||| |||||||| ||||| || |||||||||||||||||||||||||||||||| || || |||||||||||||||||||| |||||||||
---gtatccactctattttacagttcattctgcaatggccattgctgtattataattcaaactgaggcatgtggtttttgtgtattgtgacatgct-agAGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAG

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7

gtatttcttgctctgttccacagttcattttgca-cacttgtgttattttctgaacttggattcatgatatttatgtattcaatcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
||||    | |||| ||| |||||||||| ||||     ||| || |  |   ||||  |    ||| | | | ||||||    | |  | ||||||||||||| |||||||| ||||| ||||||||||||||||||||||||||||| |||||  | || ||||||||||||||||||||||||||||||
gtatccact-ctctattcgacagttcattctgcaatggctgtattgtaattcaaactgaggcatatggtttctgtgtattgtgccatgct-agAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 8

-------------------------------------------------gtatttct-tgctctgttccacagttcattttgcacacttgtgtta-ttttctgaacttggattcatgatatttatgtattcaatcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
                                                 |||| |   | |  |  |      || || |      ||||  | | ||||||  |  |   ||  | ||   |||  |||    ||| |  ||||| | ||||| |||||||| ||||||||| | ||||||||||||||||||||  ||||||| ||||| ||||| |||||||| || ||||| || |||
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagctctttgggtatcttaattcattaatatttttttaatgtcatgtgcttgcttaaattttctacagattatttactcatggctat-catttttccttttgcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTTGATTTTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8

---------------------------------------gtatttcttgctctgttccacagttcattttgcac-acttgtgttat--tttctgaacttggattcatgatatttatgtat---------tcaatcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
                                         || | | | | | |||     || || |||      ||||  | |  || || || ||   | ||   |||||| | ||         |  | |||    ||||| | ||||| |||||||| ||||||||| | ||||||||||| || |||||  ||||||| ||||| ||||| |||||||| || ||||| || |||
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 8

gtatttcttgctctgttccacagttcattttgcacacttgtgttattttctgaacttggattc---atgatattta----tgtattcaatcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
    |   | || |   | |    ||      | ||| | |   || |||    | || ||||   |   |||||     | |||  || ||     ||||| | |||||||||||||| || |||||  | || ||||||||||| ||||| ||||||||||| || ||||| |||||||| ||||| || ||||||
---gtgagtactttacccaaagtatctaacatcgcacctataagatattcatctcatgaattctgcagcgtatttgaatttttatgtaaactgaggcagAGTCTTATGGAGTATGAAGAGCACGAAAAACGTGCCTGGAGTGTTGACTTTTCACGAACAGAACCATCAATGCTTGTATCTGGTAGTGACGACTGCAAG

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 8

-gtatttct--tgctctgttccacagtt--cattttgcacacttgtgttattttctgaacttggattcatgatatttatg-tattcaatcttcttta---gAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
 ||  ||    ||     |||     |   || |    | |  | |||  || | |  |  |  ||  || |||| |||| || | ||| || ||||   |||||||||||| |||||||| ||||||||  | |||||||||||||||||||| || ||||||||||| | ||| |||||||| ||||||||||| |||
ggtcctttgaatgaaaaattctgggctcgccactgactatagatttgtccttgtatatatatatatatat-atatatatgctaataaatgttttttatcagAGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAG

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 8

------------------------------------gtatttcttgctctgttccacagttcattt---tgcacacttgtgttattttctga--acttggattcatgatatttatgtattcaatcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
                                     ||  || |  | ||  | |  ||| || |   | |||| || | | |  | |  |  | || || |  || |   || | ||||  | |  | |||||||||||||| || || || ||||||||| |||||||||||||||||||||| || || ||||| || ||||| ||||| || |||||||| ||||||
gtagaaattgtatctcttctcttctgttaatctcaattacatcata-tatgcacaaatgttgatctgcattcacaattttctaacctcccaatgatttcgagtt-tgttcactaag-attctttttcttctagAGTGTGATGGAATACGAGGAGCATGAAAAGCGAGCATGGAGTGTTGATTTTTCACGCACTGAACCTTCAATGCTCGTATCCGGCAGTGATGACTGCAAG

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S25_325V6.1 (Physcomitrella patens), 3'ss of exon 8

-------------------------------------------------------------------------------------------gtatttcttgctctgttccacagttcattttgcac-acttgtgttattttctgaacttggattcatgatat-ttatgtattcaatcttcttt----agAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
                                                                                           ||  |  |   || | |    |  |  |   |||   |||  | | |    |     |  ||   ||| || || ||  | | ||| | | |    ||||||| ||||||||||| || || || ||| | || ||||||||||| ||||| || || || || || ||||| || ||||| ||||||||| |||||
gtaggcttgaaaatttggccacttaacataggttcgttgatgatgtccttaattgtggttccagaatgagcgacatatagctttacaatgtgtcatattcattcggatttttaaattttgacgcattgcttcggatgtacggtttgtctaaatatttgacatgttctgcttgccatcatatattaccagAGTGTCATGGAGTATGAGGAGCACGAGAAGCGTGCCTGGAGTGTTGACTTTTCCCGGACGGATCCTTCAATGCTGGTCTCTGGAAGTGATGATGGCAAG

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 8

----------------------------------------------gtatttcttgctctgttccacagttcattttgcacacttgtgttattttctgaacttggattcatgatatttatgtattcaatcttcttt---agAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
                                              | |||  ||  |    |     | ||  |||| |      |  || ||  ||  |   || |    |    | ||  |||||  || |||   ||||  | ||||| ||||| || ||||||||||| || |||||||| |||||||| ||||| || ||  | |||||||| || || ||||||||| |||||
gtctgtccctcattttgatgacgttaagttgaagttaccaccccttgaattatttttttgtgtatgttggtctgtttgaagttcacttctagttaatgtgcggtgaatggccagggatttgacttcaaattttttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S180_148V6.1 (Physcomitrella patens), 3'ss of exon 8

------gtatttcttgctctgttccacagttcattttgcacacttgtgttattttctgaacttggattcatgatatt--tatgtattcaatcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
      |        |  |  | | | ||   | || | ||    ||    ||| ||    ||   |   | || ||  || ||| |   | |  |  ||||||||||||| ||||| |||||||||||| | || |||||  | ||||||||||| ||||| || || ||||| || ||||| ||||| ||| | |||
atacaagatgagggggagcaatcctagagaaaaattagtacgtgagtaaggtttacttgtgttacttatgttatcttcctaagtaatttgtttcgtgcagAGTGTGATGGAATATGAGGAACATGAAAAGCGTGCTTGGAGCATCGATTTTTCTCGTACAGATCCATCAATGCTGGTTTCTGGAAGTGACGATGGAAAG

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 8

----------------------------------------------------------------------------gtatttcttgctctgttccacagttcattttg-cacacttgtgttattttctgaacttggattcatgatatttatgta----ttcaatctt-ctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
                                                                                   |  | ||   ||    |   | | |       ||   | | ||      |   |      |  | |  ||     |  |||  | ||  ||||  | | |||||||||||| ||||||||||| ||||||||||| |||||||| ||||| || ||| | ||| |||| || || || |||||| |||||
gtttgttttcattatgctcatgccgaagtcatagatatgtcttgatgatgtaaaatccgggctttaggtacctcacccgcccatcacactcccccttgatgtgtgtaggtgtgtctgacgtgtctttctggttcacacaggcaagttctcagttgacttgtaatgatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S154_52V6.1 (Physcomitrella patens), 3'ss of exon 8

--gtatttcttgctctgttccacagttcatttt-gcacacttgtgttattttctgaacttggattcatgatatttatgtattcaatcttcttt--------agAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
  | |    | |     |  || ||   |   | |||||     |    |||      | | ||||||   ||||   |  | ||   | |||        ||  ||||||||||||||| |||||||| ||| |||| ||||| || || |||||||| ||||| || || ||||| || ||||| || |||||| | |||
cggaagcggtcgagtgatatcagagaaaaaagtagcacagaaaggggggtttt---gttggcattcatatcatttccctgcttaagtgtttttggtcatgcagGCTGTGATGGAGTATGAGGAACATGAGAAGCGAGCTTGGAGCGTAGACTTTTCTCGTACAGAGCCATCAATGCTGGTTTCTGGAAGCGATGATGGAAAG

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|2310219|gb|C26374.1|C26374

EST:     GTCCAAACCCGCCAG                         AGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTT
genomic: GTCCAAACCCGCCAGgtatttcttg ... tcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTT

EST: gi|33676005|gb|CF304244.1|CF304244

EST:     GCAGCGACTATGAGGGTATAGTAACTGTTTGGGATGTCCAAACCCGCCAG                         AGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTT
genomic: GCAGCGACTATGAGGGTATAGTAACTGTTTGGGATGTCCAAACCCGCCAGgtatttcttg ... tcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTT

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: 66 (upstream exon), 73 (downstream exon)
Score: 30

TAAACTCAGCTGCCTTAGCTGGAACAAGTACTCAAAAAATGTTATAGCAAGCAGCGACTATGAGGGTATAGTAACTGTTTGGGATGTCCAAACCCGCCAGgtatttcttg ... tcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgttattttctgaacttggattcatgatatttatgtattcaatcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG