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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctaagttgatgtttgcaggcattcttcttagcttgtttacttctttattccactgcaaaggtcactgaatccgcgttcacgatttcctgatgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG

Basic information

species Physcomitrella patens
transcript PP1S65_136V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S65_136V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA09G36870.1 (Glycine max), 3'ss of exon 3
gctaagttgatgtttgcaggcattcttcttagcttgtttact-tctttattccactgcaaaggtcactgaa--tccgcgttcacgatttcctgatgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG
               | |||  || || ||   |  | |||| | | |      ||| || ||| | ||||  ||  | |       ||  | || ||   ||||| || | ||||| |||||||||||||| || ||||||||||| || |||||  |||||||||| || || || | |||
---------------gtaggt-ttttttttccttcctatactatatgttgagttctgtaatggt-attgaatgtctacttatttcgcttttttatttcattagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: PP1S65_136V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA09G36870.2 (Glycine max), 3'ss of exon 3
gctaagttgatgtttgcaggcattcttcttagcttgtttact-tctttattccactgcaaaggtcactgaat--ccgcgttcacgatttcctgatgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG----
               | |||  || || ||   |  | |||| | | |      ||| || ||| | |||||  |  | |       ||  | || ||   ||||| || | ||||| |||||||||||||| || ||||||||||| || |||||  |||||||||| || || || | |||    
---------------gtaggt-ttttttttccttcctatactatatgttgagttctgtaatggt-attgaatgtctacttatttcgcttttttatttcattagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGGTAT

upper sequence: PP1S65_136V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
gctaagttgatgtttgcaggcattcttcttagcttgtttacttctttattccactgcaaaggtcactgaatccgcgttcacgatttc--ctgatgtc---tgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG
     |||  |||||  |   |   |  ||  ||||   || | |    |  |    | |  |   | |||   |||  |  |||     || | |    |  ||||| |  | || || ||||| |||||||| ||||| |||||||||||||||||  |||| || ||||| || || |  ||
-----gttagtgtttataataagagtgttttacttggaaacatgtaacctggaaaatacacatatttaaataaccgtgtatcattgtgtttggtataatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG

upper sequence: PP1S65_136V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 6
gctaagttgatgtttgcaggcattcttcttagcttgtttacttctttat-tccactgcaa--aggtcactgaatccgcgttcacgatttcctgatgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG
    | | ||| | |  |   ||   | |  |  ||| |   | | | | |  ||||      ||| | | ||      |||  |  ||  ||||      ||||| || | ||||| ||||| |||||||| || ||||||||||||||||||||  | || || || || || || |  ||
--gtaatagatatctatatatatctgtgtgtgtgtgtgtgtgtgtgtgtgtaaactgttgttgggttaattaaattatattcctgcatt--tgat-----tagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG

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|37821832|gb|BJ579898.1|BJ579898
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|162169289|gb|FC345451.1|FC345451
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|162157953|gb|FC334406.1|FC334406
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|37837336|gb|BJ595344.1|BJ595344
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|162154178|gb|FC330621.1|FC330621
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|162169288|gb|FC345450.1|FC345450
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|162234376|gb|FC410122.1|FC410122
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|162183538|gb|FC359012.1|FC359012
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|37828721|gb|BJ586733.1|BJ586733
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|208382679|gb|DC919833.1|DC919833
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|162191096|gb|FC367358.1|FC367358
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|162206922|gb|FC383499.1|FC383499
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|67699908|gb|BJ960141.1|BJ960141
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|162207651|gb|FC383528.1|FC383528
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|37823102|gb|BJ581168.1|BJ581168
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|67723772|gb|BJ974031.1|BJ974031
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|162207650|gb|FC383527.1|FC383527
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|162262026|gb|FC437873.1|FC437873
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|37842238|gb|BJ600246.1|BJ600246
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|37834954|gb|BJ592966.1|BJ592966
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|18334496|gb|BJ166513.1|BJ166513
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACCTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
EST: gi|37852444|gb|BJ610452.1|BJ610452
EST:     CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAG                         ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT
genomic: CAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAAT

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: 35 (upstream exon), 35 (downstream exon)
Score: 24

GTCGTCATTGGTGGTGGTCAGGAAGCTTCACAGGTGACAATGACAAGCACGCGAGTTGGAAAGTTTGAGGCGAAGTTTTTCCACAAGgtcggtgttc ... atgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattccactgcaaaggtcactgaatccgcgttcacgatttcctgatgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG
                                        tcctgat  putative branch site (score: 24)