ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaatttcctaatatttacctgttcattaaaattcatagggatcatttgatttcaaccatacaagcagtagtttgattgctaaatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG

Basic information

species	Oryza sativa
transcript	LOC_Os04g55260.1
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G882708_T01 (Zea mays), 3'ss of exon 1

gtaatttcctaatatttacctgttcattaaaattcatagggatcatttgatttcaaccatacaagcagtagtttgattgctaaatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG
                   ||  | |   |  ||| |      |  | |||||||| |||| ||||| || |||||| | |||| || ||||||| ||||||| || | |||| |||||||| || || ||||| || |||||||||||||||||||| ||||| || || || |||||||| |||||||||||||||||||||||||||||  ||||||
------------------actactgacatatgttcctgaaagcc--tagatttcaatcataaaagcaatactttgatagttaaaggtaactcatttttctcttatgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACAGTGCTGTCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGTTTTACTTG

upper sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G882708_T03 (Zea mays), 3'ss of exon 3

-----------------------------------------gtaatttcctaatatttacctgttcattaaaattcatagggatcattt------------gatttcaaccatacaagcagtagtttgattgctaaatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG
                                          |  |   || |     |  ||||  | ||||   |  |  ||   ||            |||||||| |||| ||||| || |||||| | |||| || ||||||| ||||||| || | |||| |||||||| || || ||||| || |||||||||||||||||||| ||||| || || || |||||||| |||||||||||||||||||||||||||||  ||||||
gtaaactttgcatgttaatttgtaattcctggggactagaaatgttcatctgaataacatttgtttctcaaaaactactgacatatgttcctgaaagcctagatttcaatcataaaagcaatactttgatagttaaaggtaactcatttttctcttatgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACAGTGCTGTCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGTTTTACTTG

upper sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 2

---------------------------------------------------------------gtaatttcctaatatttacctgttcattaaaattcata--------gggatcatttgatttcaaccatacaagcagtagtttgattgctaaatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG
                                                                ||| ||  | | ||||   | |  |  |  | | |||         | |    |  ||||||| | || ||||| || |||||| | |||| || ||||||| |||||||  | | |||| |||||||| || || ||||| || |||||||||||||||||||| ||||| || ||||| |||||||| ||||| |||||||||||||||||||||||  ||||||
gtaattttacaatggctttgcatgttaatttgcaattccaggggacttgaaatgttcatgtgaataacttt-tgacatttgtttctcaaaaactactgatatatgtttcagaaagcctaaatttcaatcgtaaaagcaatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG

upper sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G14010.2 (Glycine max), 3'ss of exon 1

gtaatttcct-aatatttacctgttcattaaaattcatagggatcatttgatttcaaccatacaagcagtagtttgattgcta--aatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG
|||| |  || || ||| |  | || |||   | | |    |  |    |  | ||    | ||     |||| || |   ||  | ||||| |  ||    || | | | |  ||  | |||||  | |||||||| || |||||| |||| || ||||| ||||| || ||| | || || || ||||||||||||||||| |||||||||||| |  | |
gtaagtaactcaagattgatatcttgatttgtagttaagcagtaccaaagcatgcataggttcagtgtttagtctgttgtatagtagtgttatttttttaattcctttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTATTGTCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGTTTTTGG

upper sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G32170.1 (Glycine max), 3'ss of exon 2

gtaatttc-ctaatatttacctgttcattaaa-attcatagggatcatttgatttcaaccatacaagcagtagtttgattgcta--aatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG
|| |      ||| ||| |  | |  |||    | | |    || |    |  | ||    |   |    |||| || |   ||  | ||||| |   |    || | | | |  ||  | |||||  | |||||||| || |||||  |||| |||||||| ||||| || ||| |||| || || ||||||||||||||||| ||||||||||||||  | |
gtgaggaagttaagattgatatctcaattttgtagttaggcagaaccaaagcatgcataggtttgatgtttagtctgttatatagtattgttattttattgattcatttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCGCGAACAAGTGTTGCAAGTACAACAGTATTATCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGCTTATGG

upper sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G06930.1 (Glycine max), 3'ss of exon 3

gtaatttcctaatatttacctgttcattaaaat-tcatagggatcatttgatttcaaccatacaagcagtagtttgattgctaaatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG
     | |  |||   ||  | ||| | ||  | | |||   ||||||| ||||  |   | |   ||| |||  | ||  |      || | ||| |  ||   || ||        |||||  | ||||| || || |||||| |||| |||||||| ||||| || ||  |||| ||||| |||||||| |||||||||||||||||||   |  | |
-----tgcaaaattaatattttttcttcaagttgttatacacatcattt-attttgattttgctttcagaagt--ggttctt------tattaattttcttccgttgcttt-------cagTATCTATCAAACGCTGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTGTTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG

upper sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G07010.1 (Glycine max), 3'ss of exon 2

gtaatttcctaatatttacctgttcattaaaattcatagggatcatttgatttcaaccatacaagcagtagtttgattgctaaatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG
             ||| |  ||     | |||||      |||  ||| ||      | ||  || |    || ||     |   |     | || ||   ||   | |  ||  | |||||  | |||||||| || |||||| |||| |||||||| ||||| || ||| |||| ||||| |||||||| |||||||||||||||||||   |  | |
------------cattga--tgcatgctgaaattt-----gatgtttttatgctgttc-tatgagaaaactttagaaaagcagcagcggtgctttattaattttcttctgttgctttcagTATCTATCAAATGCAGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTATTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG

upper sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G32140.1 (Arabidopsis thaliana), 3'ss of exon 2

gt-aatttcctaatatttacctgttcattaaaattcatagggatcatttgatttcaaccatacaagcagtagtttgattgctaaatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG
|| ||||| ||   || | |  |||   |    || || | | |    |||    ||   | |      |  ||| |   ||   | ||  | |||  | |  | | ||| ||| || |||||  |||| ||||| || |||||  | || ||||| || |||||||||||| | |||||||| || ||||| || ||||| |||||||||||  |  | |
gtgaattttctttgatatgctcgttgtattgttttgatggtggt-gcctga----aagtgtcc------tcttttaaac-cttggtattgat-atttgtttgctgtttttgatg-atacagTATCTGTCCAATGCTGCTCTTGCTCGTACAAGTGTGGCAAGTACTACTGTATTGTCTTCAACCTCGGGACTGTTTACTCTGTTCATTGGTGTATTTTTGG

upper sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2

gtaatttcctaatatttacctgttcattaaaattcatagggatcatttgatttcaa-ccatacaagcagtagtttgattgctaaatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG
            | | |   |    |||  | || | |  | |  |     || ||  | ||   | || | ||         |  ||   | ||| |  | |||| |||  |    |||||| || |||||||| ||||||||| | || |||||||||||||| || || ||||||||||| ||||||||||||||||||||||||||||  ||  | |
------------tgtct-tttagggattctattttacaatggtagtccaggttaaagtcctatgtgaaggaattcaga----gagagtacttgattgtgattttctatttttt----gcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG

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|29688788|gb|CB685063.1|CB685063

EST:     AGATTGCAATGTATGGCTTGTATCTTTGTCCCATATGGTTTGTGACGGAG                         TACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTA
genomic: AGATTGCAATGTATGGGTTGTATCTTTGTCCCATATGGTTTGTGACGGAGgtaatttcct ... atggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTA

EST: gi|88542773|gb|CI472121.1|CI472121

EST:     AGATTGCAATGTATGGGTTGTATCTTTGTCCCATATGGTTTGTGACGGAG                         TACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTA
genomic: AGATTGCAATGTATGGGTTGTATCTTTGTCCCATATGGTTTGTGACGGAGgtaatttcct ... atggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTA

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: 61 (upstream exon), 74 (downstream exon)
Score: 19

AATCACTGAATTCGATGACGTTTTGAAGGAGCAAGAACTTTCCACTAAGGAGATTGCAATGTATGGGTTGTATCTTTGTCCCATATGGTTTGTGACGGAGgtaatttcct ... atggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cagtagtttgattgctaaatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG