ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgtacctccaattggcaatcttaaaattttatctcttacacctttttctcttgccatgcaggacacattttctgtcattaaagcaacttaaat...

Basic information

species	Physcomitrella patens
transcript	PP1S398_18V6.1
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os05g44050.1 (Oryza sativa), 5'ss of exon 4

CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgtacctccaattggcaatcttaaaattttatctcttacacctttttctcttgccatgcaggacacattttctgtcattaaagcaacttaaat
 || |||||||| |||||||| ||||| || || ||||| || |||  |||||||||||||||||| ||| | |||||||| || |||||| | ||||| ||||  |  |  ||  |||| |  ||     |||  | ||  ||    || | || |||   |||   |||   ||| | |                   
ATTCTACCGTGGAGCAGATTGCTGTGTTCTAGTTTATGATGTCAATTCTATGAAGTCATTTGATAATCTTAACAACTGGCGTGAAGAATTTCTAATTCAGgtaatgtgttttctataattagtcat----gaatcatgtcattt----ctgtctcactttggatgtttgac---tttacag-------------------

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G158887_T02 (Zea mays), 5'ss of exon 3

CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgtacctccaattggcaatcttaaaattttatctcttacacctttttctcttgccatgcaggacacattttctgtcattaaagcaacttaaat
 || ||||| || ||||||||||||||||| |||||||| ||||||  |||||| |||||||| |||||  | |||||||| || || ||| | ||||| || |  |    ||     ||    |  | |   |   | |  |     |||||| |||  |  || | |   |  | |                      
ATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCATTTGACAACCTGAATAACTGGCGAGAAGAGTTTCTAATTCAGgtgaaatatctccaatggtttattagttcagtctcacagcaatcctgtctttttatctaactttggatgtttccctctgcag------------------

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM5G811797_T01 (Zea mays), 5'ss of exon 4

CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgtacctccaattggcaatcttaaaattttatctcttacacctttttctcttgccatgcaggacacattttctgtcattaaagcaacttaaat
 || ||||| || ||||||||||||||||| |||||||| ||||||  |||||| || |||||||| ||| | |||||||| || || ||| | ||||| || |  |  |  |  |  ||    |  | |    || |  ||| |||  |  |     | |  |      | |  |  || |   |    ||  ||  | 
ATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCGTTTGATAATCTTCACAACTGGCGTGAAGAGTTTCTAATTCAGgtgaaatattttcaacggtttattagttcagtgattcag-tctcacaattcataacaatcctgttttttcccc--taactatggatgtttcactttgcag

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA12G04830.1 (Glycine max), 5'ss of exon 4

CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaag--tttgtacctccaattggcaatcttaaaattttatctcttacacctttttctcttgccatgcaggacacattttctgtcattaaagcaacttaaat
 || || |||||||| ||||||||||| ||||| ||||| ||||||   ||||| |||||||| |||||| | |||||| |||| |||||| ||||||||||| |  ||| | ||||   ||   ||| ||   |   ||| |  | ||  |||| |   |   | |  |         | || ||                
TTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCAATGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgcttttattcctctctttataaattttctcaagctatgttgtgcagattttacaacttttaagatgtgtgatcactttggcag---------------

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA11G12630.4 (Glycine max), 5'ss of exon 4

CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgtacctccaattggcaatcttaaaattttatctcttacacct-ttttctcttgccatgcaggacacattttctgtcattaaagcaacttaaat----
 || || |||||||| ||||||||||| ||||| ||||| ||||||   ||||| |||||||| |||||| | |||||| |||| |||||| ||||||||||| | || ||   |    ||       |||  |||| ||  ||  | || || ||||  || |||  | ||| |||||    | || |||     | |      
TTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCGATGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgcttttattcctttctg-----tataattttttctcagttttatctattatctcaagctatgttgtacagattttacaacttttaagatttgtgatcactt

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA11G12630.1 (Glycine max), 5'ss of exon 4

CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgtacctccaattggcaatcttaaaattttatctcttacacct-ttttctcttgccatgcaggacacattttctgtcattaaagcaacttaaat----------
 || || |||||||| ||||||||||| ||||| ||||| ||||||   ||||| |||||||| |||||| | |||||| |||| |||||| ||||||||||| | || ||   |    ||       |||  |||| ||  ||  | || || ||||  || |||  | ||| |||||    | || |||     | |            
TTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCGATGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgcttttattcctttctg-----tataattttttctcagttttatctattatctcaagctatgttgtacagattttacaacttttaagatttgtgatcactttggcag

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA07G00660.1 (Glycine max), 5'ss of exon 4

CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtt--tgtacctcca-attggcaatcttaaaatttt------atctcttacacctttttctcttgccatgcaggacacattttctgtcattaaagcaacttaaat
 || ||||||||||||||||| ||||||||||| ||||| || || || ||||| || ||||| |||||| |  ||||||| || |||||| | ||||| |||| ||   ||| ||||| ||   |  | || ||  |        | ||| | ||  | |||   || |                                       
TTTCTACCGTGGTGCAGATTGCTGTGTCCTTGTTTATGATGTAAACGTCATGAAATCCTTTGACAACCTTAACCACTGGCGAGAAGAATTTCTTATTCAGgtaatttatggtatctccatatcacctttattgaagatcagagagaaactcatgcaaatattttattttcag-------------------------------------

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA08G21940.1 (Glycine max), 5'ss of exon 4

CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgtacctccaattggcaatcttaaaattttatctcttacacctttttctcttgccatgcaggacacattttctgtcattaaagcaacttaaat
 || ||||||||||||||||| ||||||||||| ||||| || || || ||||| || ||||| |||||| |  ||||||| || |||||| | ||||| |||| ||  |    ||| |   |  | ||    | |  ||  |   |||||| |       || |   || ||   |  ||  | ||    |  || |  
TTTCTACCGTGGTGCAGATTGCTGTGTCCTTGTTTATGATGTAAACGTCATGAAATCCTTTGACAACCTTAACCACTGGCGAGAAGAATTTCTTATTCAGgtaatttattttaaccactctcctgttttgtggtatc-tccatattacctttattgaagatca-gtgagaaac---tcatgcaaatattttattttcag-

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv09s0002g04220.t01 (Vitis vinifera), 5'ss of exon 4

CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgtacctccaattggcaatcttaaaattttatctcttacacctttttctcttgccatgcaggacacattttctgtcattaaagcaacttaaat
 ||||| ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||||||||||| ||| | |||||||| || || ||| ||||||| |||| |||   | | ||        ||| | |||  |  |     ||  || |                ||   | || |||  ||   |    | |   
TTTTTATCGTGGTGCAGACTGCTGTGTTCTTGTGTATGATGTGAATGTGATGAAATCATTTGATAATCTTAACAACTGGCGAGAAGAGTTTCTGATTCAGgtaatttt---ctttcatactctcttctgagaatcctccc-----cattttatagaaccaatgactgaaacttgtcttttgtggttttggtg-ttcag--

upper sequence: PP1S398_18V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv03s0063g02420.t01 (Vitis vinifera), 5'ss of exon 5

CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgtacctccaattggcaatcttaaaattttatctcttacacctttttctcttgccatgcaggacacattttctgtcat-taaagcaacttaaat----
 || ||||||||||| ||||| ||||| ||||| ||||| |||||||| |||||||||||||| || ||  | || ||| |||| |||||| | ||||| ||| |||  ||  | |  || | |   || |  |||   | |  |       | ||    | ||| |   | | ||||    |||  |   || | | | |    
TTTCTACCGTGGTGCTGATTGCTGTGTTCTTGTATATGATGTTAATGTGATGAAGTCATTTGACAATCTAAACAATTGGAGGGAAGAATTTCTCATTCAGgta-gttcttatgttcttttagtatattttacttttggccacagaagagggctact---acgatg-aaacctctttttggaacatgcatgtcaccatgagttctt

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|162275204|gb|FC451180.1|FC451180

EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA

EST: gi|162239905|gb|FC415744.1|FC415744

EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA

EST: gi|22491664|gb|BU051587.1|BU051587

EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA

EST: gi|162278758|gb|FC454868.1|FC454868

EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA

EST: gi|37826297|gb|BJ584309.1|BJ584309

EST:     AATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: AATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA

EST: gi|162239904|gb|FC415743.1|FC415743

EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA

EST: gi|100394822|gb|BY989942.1|BY989942

EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA

EST: gi|208390030|gb|DC938085.1|DC938085

EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA

EST: gi|208365879|gb|DC951136.1|DC951136

EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA

EST: gi|18342622|gb|BJ174657.1|BJ174657

EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA

EST: gi|100391677|gb|BY989497.1|BY989497

EST:     TGAAGGCATTTGATAACCTTGTAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGAT
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGAT

EST: gi|162278757|gb|FC454867.1|FC454867

EST:     TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAA                         GCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA
genomic: TGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAA

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: 31 (upstream exon), 35 (downstream exon)
Score: 13

CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgt ... ggtgttgcagGCAAGCCCATCCGATCCAGATAATTTTCCTTTTGTGGTCCTAGGCAACAAAGTTGACGTGGATGGTGGCAACAGTCGAGTG