ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatcctgttaattgaaatctttaattttcgtttggtacttgaaacattgtggagtgggattgacctattgggtataaaatgatgtatgattgtatgcctaactgttttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAGTATT

Basic information

species	Oryza sativa
transcript	LOC_Os01g39310.3
intron #	20
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM5G873287_T01 (Zea mays), 3'ss of exon 2

------------------------------------------------gtatcctgttaatt-------gaaatctttaattttcgtttggtacttgaaaca----------ttgtggagtgggattgacctattgggtataaaatgatgtatgattgtatgcctaactgttttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAGTATT
                                                  | | |||  |||        |||||  |   ||| ||||  ||||  | ||           ||| | ||||||| ||    | |   |   | | |||       | | |||  |||    ||||| || |||| ||||||| |||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||  | |      
gtatctccacatttccattccaccagttaactgatatgtgtgctattgacaccttgtggatttcatctcaaaatccctctattttgtttattactcaatactcatgattttcttgggaagtgggactggttcacttaattagagacgat------ctatctgctaaaca---ttactgttgccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTACCACCTCCATGGGCACTTGCTGCAATGGCTATTCTTGGATTCAACGAGTTCATGACATTACTGAG-----

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 20
lower sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 19

----------------------------------------------gtatcctgttaat-------tgaaatctttaattttcgtttggtacttgaaacattgtgg--agtgggattgaccta-ttgggtataaaatgatgtatgattgtatgcctaactgtt--ttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAGTATT
                                                | | |||  ||         |||||  |   ||| ||||  |||||   |  || |||  ||||||| ||||| | ||   || | | | | || |||  | |   ||| ||| |  ||||| || |||| ||||||| |||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||  | |      
gtatctccacgtttccattccaccagttaactgatatgtggtattgacaccttgtggatgtcatttcaaaatccctctattttgtttattacttatgattttttgggaagtgggaatgacccacttaaataaatattaaagtttga--gaagatctatctgctaattactgttgccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTTATGACATTACTGAG-----

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G350256_T01 (Zea mays), 3'ss of exon 3

gtatcctgttaattgaaatctttaattttcgtttggtacttgaaacattgtggagtgggattgacctattgggtataaaatgatgtatgattgtatgccta-actgttttactttttccttcatcagGAGGCAAATAAGAGGAACA-ACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAGTATT
                                                                              |   | |||||  | | | |||| |   | ||| | |     | ||     | || ||       ||| |  |       | |  |   |     |  |   ||||| |||||||||||||||||||||| |||||| | || |      
---------------------------------------------------------------------------cttagcaacgtatggatatttacctatataatattagtgtcatagtgatattttgtcacatggattctacatattatatatctctattttttta--ttcccgTGACAATGTCTATCCTTGGATTCAACGAGTTTATGACACTATTGAT-----

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 20
lower sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20

gtatcctgttaattgaaatctttaattt-tcgtttggtacttgaaacattgtggagtgggattgacctattgggtataaaatgatgtatgattgtatgcctaactgttttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAGTATT
                  | | ||  || | || |  |   | |    || |  | |  |  | ||     |   |  || ||| || | | | |      |      ||   |||        ||||| || ||     |||| ||||||||||||||||||||||||||| |    ||  ||| | | |||||||| || || || |||||  | ||||      
------------------tttctagcttcttgtctcctttctcatctgttctttaatcag-ctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggattt--------cagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG-----

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|29641074|gb|CB646081.1|CB646081

EST:     AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAN                         GAGGCAAATAAGAGGAAACA-CAACTGGCTGCCACCTCCAT
genomic: AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAGgtatcctgtt ... ccttcatcagGAGGCAAATAAGAGGAA-CAACAACTGGCTGCCACCTCCAT

EST: gi|157650537|gb|EX450171.1|EX450171

EST:     AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAG                         GAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGTACTTGCC
genomic: AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAGgtatcctgtt ... ccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC

EST: gi|38474188|gb|CF958320.1|CF958320

EST:     CATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAG                         GAGGCACATAAGAGGAACAACAACTGGCTGGCACCTCCATGGGCACTTGCC
genomic: AATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAGgtatcctgtt ... ccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCC

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: 75 (upstream exon), 75 (downstream exon)
Score: 78

AGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGGAGGCAATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTGCTCAGgtatcctgtt ... ccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAGTATT

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ggtataaaatgatgtatgattgtatgcctaactgttttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAGTATT