ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gttagtgttctggtttgcgtattgggagtcaatatagcttatggcagtaatgcaggcttcagccctccatttatggcttgtaataattaagcaaagcattgcactatttgtcattctgtacctctcagttctctgaccactgattacttgcattgttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAGCTTATTCAAAAGTATCTTGGTGATGGTCCCAAACTAGTCAGGGAACTGT

Basic information

species	Oryza sativa
transcript	LOC_Os07g49150.1
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 2

gttagtgttctggtttgcg----tattgggagtc---aatatagctta-tggcagtaatgcaggcttcagccctc-----catttatg---------gcttgtaataattaagcaaagcattgcactatttgtcattctgtacctctcagttctctgaccactgattacttgca-ttgttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAGCTTATTCAAAAGTATCTTGGTGATGGTCCCAAACTAGTCAGGGAACTGT
|| |||| || || ||||     ||   |   ||   ||||| ||||| ||  | |    ||||||||   ||||      ||||            | || |   ||||| |||     ||   ||| |   || | |  |  |  ||  |   ||  || ||| |||||| |  ||||  ||||||||||||| || || ||||| || ||||||||||||||||| || ||||| |||||||||||||| ||||| ||||||||||| |||||||| ||| |||
gtcagtgctcaggcttgcaagcatacaagatatctgtaatattgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcagGCTGTTGCCAATTCAACATCTGCGACTTTCTTGCGTGTTGTCGGTAGTGAACTTATTCAAAAGTACCTTGGGGATGGTCCCAAGCTAGTCAGAGAATTGT

upper sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 2

gttagtgttctggtttgcg----tattgggagtcaatata--gcttatggcagtaatg-caggcttcagccctccatttatggcttgtaataattaagcaaagca-ttgcactatttgtcattctgtacctctcagttctctgaccactgattacttgcattgttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAGCTTATTCAAAAGTATCTTGGTGATGGTCCCAAACTAGTCAGGGAACTGT
|| ||| |||||  ||||     ||   |  |||||||||  |||||     | |  | |||||||  |   ||    | || ||     ||   ||   |  |  ||   ||| || ||| | |  |  |  ||  |   ||   | |||||||||| |   |   |||||||||| |||||||| ||||| || |||||||||||||||||||| ||||| || ||||||||||| ||||| |||||||||||||||||| | ||| |||
gtcagtattctgtcttgcaagtatacaagatgtcaatatattgcttagtattgcaggggcaggcttt-gatatctgcctttgtctatgtttatccaaattacactctttttctacttttcagttttcaaatagcatgtacttgggtagtgattacttgaaac-tgtctgcagGCTGTGGCTAACTCAACATCTGCGACTTTCTTGCGTGTTGTTGGTAGTGAACTCATTCAAAAGTACCTTGGGGATGGTCCCAAACTAGTCCGAGAATTGT

upper sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2

gttagtgttctggtttgcgtattgggagtcaatatagcttatggcagtaatgcaggcttcagccctccatttatggcttgtaataattaagcaaagcattgcactatttgtcattctgtacctctcagttctctgaccactgattacttgcattgttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAGCTTATTCAAAAGTATCTTGGTGATGGTCCCAAACTAGTCAGGGAACTGT
                                                 || ||    |||      ||  | ||  || | || |||  | |  |   || ||||     ||  | | ||     | ||     |  ||  |    ||      |  || |||||||| || ||||| ||||| ||||| || |||||||||||||| |||||  | || ||||| ||  | || |||||||| || || || |||||||| |
------------------------------------------------gatccacatctcactgtgtcaactttg--tttttattattgtgtatcg---tgtacta-----cacacagcacaatcaatttagtctaatacaaacccttt------tactttcagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT

upper sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 2

gttagtgttctggtttgcgtattgggagtcaatatagcttatggcagtaatgcaggcttcagccctccatttatggcttgtaataattaagcaaagcattgcactatttgtcattctgtacctctcagttctctgaccactgattacttgcattgttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAGCTTATTCAAAAGTATCTTGGTGATGGTCCCAAACTAGTCAGGGAACTGT
      |||   ||||   | |||    |   || ||||    |   ||||  ||  |  |   |||| |||     |  | ||  ||  ||  ||  || || | |  |       |    | ||||     | |     || ||      ||||   | |||||||| || ||||| ||||| ||||| ||||||||||||||||| ||||| || || ||||||||  | || ||||| || ||||| || || ||||| |
------gtttgtgtttatcttttgcttcttc-tagagct----gttttaatagagtttcaacatctcctttttactatctttatcttttggc--agtgtttcaatttaag-------gagtgtttcagcatcttaa-----gactatgccttttgtgtattcagGCTGTGGCAAACTCAACATCAGCAACATTCTTGCGTGTTGTTGGTAGTGAACTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTAAGAGAACTTT

upper sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 2

gttagtgttctggtttgcgtattgggagtcaatatagcttatggcagtaatgcaggcttcagccctccatttatggcttgtaataattaagcaaagcattgcactatttgtcattctgtacctctcagttctctgaccactgattacttgcattgttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAGCTTATTCAAAAGTATCTTGGTGATGGTCCCAAACTAGTCAGGGAACTGT
                                 || | || | |||||       || ||     |  || | |  ||| |  |  ||||     | | ||      |||    |  | |  | | | ||||                    || || || ||||| || || || || || || || ||||||||||||||||| || ||||| || ||||| |||||| | || ||||||||||| || || |||||||| |
---------------------------------atggattgttgcagtgt-----gcctc--tttttaatgtgtctcttatgcttgttaaattcggaactg------ttggagatgagcaagtgttatttctt------------------gttattctttcagGCAGTGGCAAATTCTACTTCAGCTACTTTCTTGCGTGTTGTCGGTAGTGAACTGATTCAGAAGTATTTAGGAGATGGTCCCAAGCTTGTGAGGGAACTTT

upper sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 2

gttagtgttctggtttgcgtattgggagtcaatatagcttatggcagtaatgcaggcttcagccctccatttatggcttgtaataattaagcaaagcattgcactatttgtcattctgtacctctcagttctctgaccactgattacttgcattgttgt-tgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAGCTTATTCAAAAGTATCTTGGTGATGGTCCCAAACTAGTCAGGGAACTGT
                                                          |  |   |  | || |    | |  |  || ||   |  ||   | ||  |  | |     |  | |      ||| |  |||    ||   ||||  |||   ||||| ||||| ||||| ||||| ||||||||||| ||||||||||| |||||| | |||||||| ||| | || ||||| || ||| |||| |||||  | |
---------------------------------------------------------ctttgttatttacttttcttatattcttgtttagttgaagatcagagtagcttccttgtcaaagttgt------tctaa--acttgcaaccctcatttatgtactcagGCAGTTGCAAACTCTACATCAGCAACTTTCTTACGTGTTGTTGGCAGTGAGTTAATTCAAAAATATTTGGGAGATGGGCCAAAATTAGTGAGGGAGTTAT

upper sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 2

gttagtgttctggtttgcgtattgggagtcaatatagcttatggcagtaatgcaggcttcagccctccatttatggcttgtaataattaagcaaagcattgcactatttgtcattctg-tacctctcagttctctgaccactgatta-cttgcattgttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAGCTTATTCAAAAGTATCTTGGTGATGGTCCCAAACTAGTCAGGGAACTGT
                                                                                                             || | | ||  | || | |     |||     | | || || || ||| |  | ||||||||||| ||||||||||| ||||| ||||||||||||||||| || |||||||||||||||||| | || || ||||| || || || ||||| || |
-------------------------------------------------------------------------------------------------------------gtaagtgtgacatcttttaaggtgctgcttcgtaactaactagctttggttctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAGCTTATTCAAAAGTATTTGGGAGACGGTCCTAAGCTTGTTAGGGAGCTCT

upper sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 2

gttagtgttctggtttgcgtattgggagtcaatatagcttatggcagtaatgcaggcttcagccctccatttatggcttgtaataattaagcaaagcattgcactatttgtcattctg-tacctctcagttctctgaccactgatta-cttgcattgttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAGCTTATTCAAAAGTATCTTGGTGATGGTCCCAAACTAGTCAGGGAACTGT
                                                                                                             || | | ||  | || | |     ||      | |||| || || ||| |  | ||||||||||| ||||||||||| ||||| ||||||||||||||||| || |||||||||||||||||| | || || ||||| || || || ||||| || |
-------------------------------------------------------------------------------------------------------------gtaaatgtgacatctttgaaggtgctacttcgtaattaactagctttggttctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAGCTTATTCAAAAGTATTTGGGAGACGGTCCTAAGCTTGTTAGGGAGCTCT

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|88406174|gb|CI593954.1|CI593954

EST:     GAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAG                         GGTGTTGCTAACTCCACATCCGCAATTTTCTTGCGTGTTGTTGGAAGTGAG
genomic: GAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAGgttagtgttc ... gttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAG

EST: gi|10931233|gb|AU161507.1|AU161507

EST:     GAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTTCCAAG                         GCTGTTGCTAACT
genomic: GAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAGgttagtgttc ... gttgttgcagGCTGTTGCTAACT

EST: gi|300216308|gb|HO088093.1|HO088093

EST:     GAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAG                         GCTGTTGCTAACTCCACATCTGCAACTTTCTTGCGTGTTGTTGGAAGTGAG
genomic: GAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAGgttagtgttc ... gttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAG

EST: gi|427421|gb|D23487.1|D23487

EST:     GAGTCATATTATACGGAGAACCTGGAACAGCNAAGACACTACTTGCCAAG                         GCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAG
genomic: GAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAGgttagtgttc ... gttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAG

EST: gi|66915039|gb|CX101887.1|CX101887

EST:     GGAGAA-CTGGAACAGGGAAGACACTACTTGCCAAG                         GCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAG
genomic: GGAGAACCTGGAACAGGGAAGACACTACTTGCCAAGgttagtgttc ... gttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAG

EST: gi|30229533|gb|CB967424.1|CB967424

EST:     GAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAG                         GCTGTTGCTAACTCCACATCTGCAACTTTCTTGCGTGTTGTAGGAAGTGAG
genomic: GAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAGgttagtgttc ... gttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAG

EST: gi|117222452|gb|CT845862.1|CT845862

EST:     GAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAG                         GCTGTTGCTAACTCCACATCTGCAAC
genomic: GAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAGgttagtgttc ... gttgttgcagGCTGTTGCTAACTCCACATCCGCAAC

EST: gi|27577327|gb|CB000022.1|CB000022

EST:     GAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAG                         GCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAG
genomic: GAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAGgttagtgttc ... gttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAG

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), 72 (downstream exon)
Score: 83

TTTGACCCATCCTGAGCTATATGAAGACATTGGCATCAGGCCACCCAAGGGAGTCATATTATACGGAGAACCTGGAACAGGGAAGACACTACTTGCCAAGgttagtgttc ... gttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAGCTTATTCAAAAGTATCTTGGTGATGGTCCCAAACTAGTCAGGGAACTGT

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtcattctgtacctctcagttctctgaccactgattacttgcattgttgttgcagGCTGTTGCTAACTCCACATCCGCAACTTTCTTGCGTGTTGTTGGAAGTGAGCTTATTCAAAAGTATCTTGGTGATGGTCCCAAACTAGTCAGGGAACTGT