ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgtagaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG

Basic information

species	Physcomitrella patens
transcript	PP1S167_51V6.1
intron #	10
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10

gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgtagaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG
            ||    ||  ||  | ||    |||| ||   ||   ||  |   |      ||   ||  |     | || | | |   |||| ||| | |||||||| |||||||||||||| || || ||||| ||||| ||||||||||||||||||||  | | ||| ||||||||||| ||  |
------------gtgagactt-tg--tcaaccgaatgactaaaaagaagccatatgatgactgatacataatct-----agctgtactctaatttt-cagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10

gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgtagaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG
        | | || | |  |   |  | ||   |  | | |||| |      ||   | ||   ||  ||  ||  |     |||  | |||||||||||| |||||||| ||||| || || || || || ||||| |||||||||||||| |||||||||||  | ||||| |||||||| || |||||
-------gtgaagtttcgtaacctgaatgatggcaaaaat-gtcaatg--ttaagacatgtcacaatctaa--tgccgtgttaattt-catcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10

gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgtagaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG
           || |   ||     || ||||   | |  ||  || ||   ||          || || | || ||  |  |||   |     || ||||| |||||||| || ||||| ||||| || |||||||||||||| || |||||||||||||||||  | ||||| ||||||||||| ||  |
----------gtgaaattctctcaactgaata-attaaaaaggaagctatttgatgaacaaaagtaatgtaattttatga--tat---cactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 10

gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgtagaaactattcgcgtc--ttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG
                 | | |     | ||   || || | |   || |    || || |||   ||  |  ||   |  || || |  |     |  |||||||||||| | ||||| || || || |||||||| ||||| ||||||||||| ||||| |||||  |||| || ||||||||||| |||||
-----------------gtttgataagtgatg-aattatgaatttctttctactgttttgtctgagttataactggttatgctttttgtttgaacgtgccagCTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAG

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10

gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttcttta-ttgaacttg--tagaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG
  ||  | |  ||| |   |||     | ||   || || | |   | |  | | || ||| |  | ||  |  ||  || |   |||    |    |  |||||||| ||| | ||||| || ||||| ||||| || ||||| ||||||||||| ||||| |||||  ||||  | ||||||||||| |||||
-gttagattcctgtgt--ttagataagtgatg-aattatgaatt--tcattctactgctttgtcgagttataactggttatattttatgtttgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10

gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgtagaaacta-ttcgcgtcttttg---cagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG
        | |  |     |  |    |||    ||||  | | | || || |      | ||||||  |  |  ||| ||||   ||   | ||||    |||||||||||| | ||||| || || || || || || |||||||| |||||||| ||||| |||||  |||||||  |||||||||| |||||
-------gttagattcccatgtttatataa-gtaatgagcaatgaatt-cctg-----ctgctttatcaag-tcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10

gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgt-agaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG
                   |    ||||  | |  ||     ||  |||   |    || | | |    | ||    |     | ||     |  |||||||| || ||||| ||||| || ||||||||||| || || ||||| |||||||| ||||| |||||  || | || ||||| ||||| |||||
------------------gtgagagcttctttctgtggc--atcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 10

---------------------gcttcaaataatgtatagctagtggctt-aatacgatgatt----agtcagttacccgagtgttttctttattgaacttgtagaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG
                     |||||   |  | |        ||  || |||    | |||      |   ||  |  |   | |    |||| || || |    | ||||    ||||   ||||| |||||| | ||||| || || || ||||||||||| ||||| |||||||| ||||| |||||  | || ||||| ||||||||||||||
gtgatttcacttcttcatgaagcttcctttttttttggtgctttgatttgaatggagttattttgggctttattgtcaaataatatgaactatttaa-ttattatcattatttaaatcttgatcagCTGTGTGATTTATATGAAAATGATTCTATCTTCGACAAATTTGAGTGTTGTCTGAGTGGAGATGGACTACGAGTGGCGACTGGTTCCTACAG

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10

------------gcttcaaataatgtat-agctagtggcttaatacgatgattagtcagtt-acccgagtgt-----tttctttattgaacttgtagaaac--tattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG
             |||   | ||| ||| | |||  |||  |||| |     ||   | || | |  |||||     ||| |  ||     | || | |    || ||   ||||   ||| | || ||| | ||||| || || || ||||| ||||||||||| |||||||| ||||| ||||| |  || || ||||||||||| |||||
gtgcgattttcttcttttga-aatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 10

gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgtagaaactattcgcgtcttt---tgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG
         |   |          |   | |   |  |     ||  | |   | |  | |||  ||   | || ||    || ||    || ||   | ||| | |||||| | ||||| || || || ||||| || || |||||||||||||| ||||| ||||| |||||||| || || ||||| |||||
------gtgagcttgctttcctcagaaaagtcttac-acagaacaacttctacattactctctgcatgctaattttaccctctgtttctttccttctctccagTTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAG

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|37827186|gb|BJ585198.1|BJ585198

EST:     TTTAAAGTCCACGAGTATTTGCGTCCAAAG                         CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGT
genomic: TTTAAAGTCCACGAGTATTTGCGTCCAAAGgtgaatcctg ... tcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGT

EST: gi|37836637|gb|BJ594645.1|BJ594645

EST:     TTAAAGTCCACGAGTATTTGCGTCCAAAG                         CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGT
genomic: TTAAAGTCCACGAGTATTTGCGTCCAAAGgtgaatcctg ... tcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGT

EST: gi|162181126|gb|FC357285.1|FC357285

EST:     AATCTTCCCCTGTGGCCGTATTTAAAGTCCACGAGTATTTGCGTCCAAAG                         CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGT
genomic: AATCTTCCCCTGTGGCCGTATTTAAAGTCCACGAGTATTTGCGTCCAAAGgtgaatcctg ... tcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGT

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: 34 (upstream exon), 32 (downstream exon)
Score: 8

TTGTGGGATGTGAACATGGAATCTTCCCCTGTGGCCGTATTTAAAGTCCACGAGTATTTGCGTCCAAAGgtgaatcctg ... tcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gttacccgagtgttttctttattgaacttgtagaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG