ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtttggattactcgtatatcagagataaaaaaaaatgatgcacacattctagatgatttcttattctgcttagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA

Basic information

species	Oryza sativa
transcript	LOC_Os01g56670.3
intron #	11
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G173868_T04 (Zea mays), 3'ss of exon 11

gtttggattactcgtatatcagagataaaaaaaaa---tgatgcacacattctagatgatttcttattctgcttagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
|||||| |||| | ||| || || |    |        ||  ||||| ||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| ||||| || ||||||||||||||||| || |||||||| ||||| || ||||| ||||| |||||||||||||
gtttgg-ttacacatatttctgataattgatgtggctttgtcgcacatattctagatgattgcttatgctgcttagatttaagGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAGTATGGTTTTACCCCTGAAGGTTTTAATCTTGCTA

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 10

-----------------gtttggattactcgtatatcaga---gataaaaaaaaatgatgcacacattctagatgatttcttattctgcttagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
                  |||    || | |||| |         |    | |||| ||     |||  | |      |  ||   ||  |   || ||||| |||||||||||| |  |||| || ||||| || |||||||||||||| ||||| |||| || |||||| || || || || || |||||||||||||
gttttcattttcctagtttttaatataatagtatttttagctgactctggataaataataatatcatggtggggataattgtaacatgtattttttcaagGTTTTAGCTGGAGATATCAATCCCGCAATTCGCACCCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACTCCTGAGGGCTTTAATCTTGCTA

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G35290.1 (Glycine max), 3'ss of exon 6

gtttggattactcgtatatcagagataaaaaaaaatgatgcacacattc--tagatgatttcttattctgcttagatttaagGTGT---------------TAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA-------
||||  |||  || | | |  || ||||    |  |   |   ||  |   || || || || |  |  |  ||  | ||| ||||               ||||||||||| |  ||||||| ||||| ||||||||||||||||| ||||| |||| || |||||| || ||||| ||  | |||||||||||||       
gttttcatttttcttgtttttgatataatggtatttttagttgactctggataaataatatcatggtggggctaattgtaatgtgtatttttgcaatgttttagCTGGAGATATCAATCCTGCAATTCGCACTCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACCCCTGAGAGCTTTAATCTTGCTAGTCTCAG

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 11

----gtttggattactcgtatatcagagataaaaaaaaat-----gatgcacacattctagatgatttcttattc-tgcttagattt---aagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
     |   ||||   ||| |  |  |  |   || | ||     | || | |  ||    |||||||  |||   || ||   | |   ||||| ||||||||||| |||||||| || ||  |||||||  |||||||||| || || ||||||  |||||| |||||||| || || |||||||||||||
gtaaatagtgattctacgtttgaccaaattgttaatatatttcaggctggaaaatttaactatgattttgtatctatgtttctctctcaaaagGTTTTAGCTGGAGACGTTGATCCAGCAATAAGAACTCACACTGCCTTCTTTAGCGTCTGGAAACGATATGGTTTCACCCCTGAGGGTTTTAATCTTGCTA

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 12

gtttggattactcgtatatcagagataaaaaa-aaatgatgcacacattctagatgatttcttattct-gcttagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
       |   |  | ||| |   ||| |  | ||||  ||||       |  || |   |  ||| |  ||| |    |||||  ||||||||||  |||| ||||| |||||||| ||| ||||||| || ||||| ||||||| |||||||||||||||||| || ||||||||||| |
------gtattttatctattatttatatattataaattttgcattgtcgattaatcaaaaccgattatcactttgg---aagGTTCTAGCTGGAGACATTGACCCTGCTATTCGAACGCATACTGCCTTTTTTAGTGTTTGGAAAAGATATGGCTTCACCCCAGAGGGTTTTAATCTTGCCA

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ28925 (Selaginella moellendorffii), 3'ss of exon 11

gtttggattactcgtatatcagagataaaaaaaaatgatgcacacattctagatgatttcttattctgcttagattta--agGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
                         |||| |  |    | |  |  || ||      || | |||| | |     | |  |||| || || |||||||| || || || | || ||||||  | || || |||  ||| ||||| || | |||||||||||||||||| ||||||||||| |
------------------------gtaaagatgatgtgttccaatgttttaac---attttgattccgatcgccataatcagGTCTTGGCAGGAGATGTAGAACCCGCTACTCAAACTCACACAGCATTTTTCTCTGTGTGGAAGAAGTTTGGCTTCACCCCAGAAGGATTTAATCTTGCAA

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ13630 (Selaginella moellendorffii), 3'ss of exon 11

gtttggattactcgtatatcagagataaaaaaaaatgatgcac-acattctagatgatttcttattctgcttagattta--agGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
                              ||| ||||||    ||| | |       || | |||| | |     | |  |||| || || |||||||| || || || | || ||||||  | || || |||  ||| ||||| || | |||||||||||||||||| ||||||||||| |
----------------------------gtaaagatgatgtgttacaatgttttaacattttgattccggtcgccataatcagGTCTTGGCAGGAGATGTAGAACCCGCTACTCAAACTCACACAGCATTTTTCTCTGTGTGGAAGAAGTTTGGCTTCACCCCAGAAGGATTTAATCTTGCAA

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|33796226|gb|CF323979.1|CF323979

EST:     CTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG                         GTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
genomic: CTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggatta ... tagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC

EST: gi|58601755|gb|CK012283.1|CK012283

EST:     CAGTCTCCAGGCATTCTGGCCAGGACTTCAG                         GTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
genomic: CAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggatta ... tagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC

EST: gi|88361880|gb|CI682051.1|CI682051

EST:     CTGTNTGGCCACTATCCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG                         GTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
genomic: CTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggatta ... tagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC

EST: gi|88394177|gb|CI684850.1|CI684850

EST:     CTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG                         GTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
genomic: CTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggatta ... tagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC

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: 41 (upstream exon), 50 (downstream exon)
Score: 4

GTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggatta ... tagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

taaaaaaaaatgatgcacacattctagatgatttcttattctgcttagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA