ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaacatttttctatgatgtcctaaactgttctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG

Basic information

species	Oryza sativa
transcript	LOC_Os03g62500.1
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G138676_T02 (Zea mays), 3'ss of exon 9

gtaacatttttctatgatgtcc---taaactgttctctcctgtgac----cattgatcttgacaataacatgtttagtcatagcgcct------tgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
     |||||  || | | |||   | | |   ||||| ||||       | ||  | |  || || |||| || || ||||||  ||      |||||||||||||||||||||||||||||||||||||||||||||| || ||||| ||||||||||| ||||| |||||||| |||||||| |||||||||
--gtgattttcttacggtatccatatgaccatatctctactgttttgctgccttcttttgcaccatgacatattgaggcatagcatctgcatcttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAACCCAAACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 9

----------------gtaacatttttctatgatgtcctaaactgttctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
                  |   || |  ||| | ||  |  | |   || | ||   |     |   |  ||||| |||  | || | ||      |  ||||||||||| |||||||| ||||| ||||| ||||||||||| || || || || || || || || || || || ||  ||||||| |||||||||
ggttttccaagttttgtcattgttctaatataaagttttgtagttcactattctcccaatggagtcatgaacaattaca-atctaatgatt-tttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAG

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 8

----------------gtaacatttttctatgatgtcctaaactgttctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
                 |  |||| ||||   ||    |    |   || |  |   |     |   |  ||||| |||  | || | ||      || ||||||||||| |||||||| ||||| ||||| ||||||||||| || || || || || || || || || || || ||  |||||||||||||||||
ttaggtttaccaagttctgtcattgttctgatataaagttttgtagactattttcccaatggagtcatgaacaattaca-atctaatgatt-tttatttcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCATGGCACAAG

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 9

-----------------gtaacatttttctatgatgtcctaaactgttctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
                   | || |   || ||   | || |  | |  | ||  |  | | ||| | ||   | |  ||| |    | |||  | | |||||||||| ||||| |||||||||||||| ||||||||||||||||| ||||| || || || || || || || || ||  |||||||||||||||||
cgtattcagtatagaagaaagcagtaacctttggattgctcag-tctgatttcgaggaaaccttggttttcttattt-catttgctttgata-tgtcatgcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 10

------------------------------------------------------------------------------------------------gtaacatttttct-atgatgtcctaaactgttctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
                                                                                                 | | |||||| | || |     ||      | | |   ||     | |  | |        |||| ||  | | |  | | |||||||||||||||| ||||||||||| |||||||| ||||||||||| |||||||| || || ||||| ||||| || ||  ||||||| |||||||||
gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttaccaccatttttgtagtaggactcgtacattctctcttcatggtttttta-attgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 8

--gtaacatttttctatgatgtcctaaactgttctctcctgtgacc---------attgatcttgacaataacat---gtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
  |  || | | | ||     |  |  |  | ||    |||| |           |   | | | | ||||| ||    | |  | | |  ||  ||||||| ||||| || || || ||||| ||||| || || |||||||| |||||||| || || |||||||| ||||| ||| |||||||||||||||||
atgctacttctatttacagaatttttgaaagctcaaatctgtcatttaaacccaaaggaagcctcagaataagattccatgtgtttaaattgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 7

---------------------------------------------------------------------------------------------------gtaacatttt--tctatgatgtcctaaactgttctctcctgtgac--cattgatcttgaca-ataacatgtttagtca-tagcgccttg----cagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
                                                                                                   | ||  || |      |  |  |      || | |    | ||||  |  |    | || |  ||  |  | | |  | | | |  ||      |||| ||||| || || ||| | || ||||| |||||||||||||||||||||||||||||||| || |||||||||||||||||||| |||||||||
gtagcttacatatggtagatgttgaggaagtgcaggggtctacagcagatgtcggtgctggtgtttgggttttgtccgtttgaaatgttgtgttgcgttgaaaggttgtagctggtacttgctcggtgtgatgttagttatgacttcgctagaatggatatgtaggacttatgggtagttgggtgttaatgttagGTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAG

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8

------------------------------------gtaacatttttctatgatgtcctaaactgtt-ctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttg-cagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
                                    ||  | |  ||   || ||      |||||| |     ||| |  || | | | ||   ||   | || ||  | ||     || ||||| ||||| || || ||  | || |||||||||||||||||||||||||||||||||||||| || || ||||| |||||||| ||||||||||| 
gtagggcacaggcgatgcacggtgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggagtgttatgat-gctgtggagtgtatgttattgaggaaaagttttgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 8

------------------------------------gtaacatttttctatgatgtcctaaactgttctc----tcctgtgaccattgatcttgacaataacatgtttagtcatagc-gccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
                                    ||  | |  ||   || ||      ||||||       |  | |||   |      ||  | ||   | || ||   ||   |  | |||||| ||||| || || ||  | || ||||| |||||||||||||||||||||||||||||||| || || ||||| |||||||| || |||||||| 
gtagggcacaggcggtgcacggcgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggggtgttatgatgctgtggagtgtgagtatgttattgaggagtacttgtgtggcagGTGTTGGGAACACCGACTCGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCGTGGCACAAA

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 7

-------------------------------------gtaacatttttctatgatgtccta------aactgttctctcctgtgaccattgatcttgacaataacat-gtttagtcatagc-gccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
                                     ||  | || |    ||  |   |       | ||||  | || |||     |||    |||  ||  | | |   || | |  | |  | |||||||||||| || || ||  | || ||||||||||||||||||||||||||||| |||||||| || || ||||| ||||| || || |||||||| 
gtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctgggttggcggtttggtttgtagctgtggtatcttgttcgtgttggatgtgagtatggcgttgaccagacgtttccgtgtggcagGTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 8

-------------------------------------------------------------------------------------------------gtaacatttttctatgatgtcctaaactgttctctcctgtgaccat-----tgatcttgacaataacatgtttagtc--atagcgcctt--gcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
                                                                                                  |   |  |     || ||         ||  |    ||  | |       ||||  ||   |    |||  ||| |  || | |   |   ||||| || || || || ||| | || ||||| |||||||||||||||||||||||||||||||| || ||||||||||||||||| || |||||||||
gtatgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgcttcgggtggtgttgcggtgatagcgcaagagtgatactgtagagcttatgagtaggcggatggtgatgttgacagGTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAG

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9

gta-acatttttctatgatgtcctaaactgttctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
|||  |||   |   || | |  |       | | |  || ||   | | |||||   |  || || ||            |||||||| || |||||||| ||  | || || ||||| ||||||||||| |||||||||||||| || |||||||| ||||| || ||||| |||||||||
gtacgcatgcattcttgctcttttttttctgttttttttgcga--gtcgctcttgctcaagacttgctt------------ttgcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9

gtaacatttttctatgatgtcctaaactgttctctcctgtgacca-ttgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
        |    |||   || |   || || | || | |  | | | | |||||   |  || || ||            |||||||| || |||||||| ||  |||| || ||||| ||||||||||| |||||||||||||| || |||||||| ||||| || ||||| |||||||||
-------gtacgcatgcattcttgctctcttttttctttttgcgagtcgctcttgctcaagacttgctt------------ttgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8

gtaacatttttctatgatgtcctaaactgttctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
               | || |      | || |  | | ||     ||     | |  | | |   || | | | |      ||||||| | || || || ||  | || ||||||||||| |||||||| ||||||||||| ||||| ||||||||||| ||||| || || |||||||||
---------------gttggctcgttgt-ttttgccttatggtggctg-----ggcgctcataaagttggacttgg------gcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG

upper sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 8

gtaacatttttctatgatgtcctaaactgttctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
               | || |      | || |  | | ||     ||     | |  | | |   || | | |        ||||||| | || || || ||  | || ||||||||||| |||||||| ||||||||||| ||||| ||||||||||| ||||| ||||| |||||||||
---------------gttggctcgttgt-ttttgccttatggtggctg-----ggcgctcataaagttggacttg------cgcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCATCCTTGGCACAAG

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|9886149|gb|AU065662.2|AU065662

EST:     CTCTGTTCCCNGGGGAAAGTGGAGTTGATCAGCTGGTCGAGATTATCAAG                         GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTAC
genomic: CTCTGTTCCCTGGGGAAAGTGGAGTTGATCAGCTGGTCGAGATTATCAAGgtaacatttt ... cgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTAC

EST: gi|88224520|gb|CI222700.1|CI222700

EST:     AGTGGAGTTGATCAGCTGGTCGAGATTATCAAG                         GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTAC
genomic: AGTGGAGTTGATCAGCTGGTCGAGATTATCAAGgtaacatttt ... cgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTAC

EST: gi|88274655|gb|CI395061.1|CI395061

EST:     CTCTGTTCCCTGGGGAAAGTGGAGTTGATCAGCTGGTCGAGATTATCAAG                         G-TTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTAC
genomic: CTCTGTTCCCTGGGGAAAGTGGAGTTGATCAGCTGGTCGAGATTATCAAGgtaacatttt ... cgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTAC

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: 59 (upstream exon), 60 (downstream exon)
Score: 22

CCTCTGTTCCCTGGGGAAAGTGGAGTTGATCAGCTGGTCGAGATTATCAAGgtaacatttt ... cgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG