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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttcttgggggtctgtcagaccaactgggcttgccacgtcaaggttatgttttgttatttgtcattgggaaaataacaagttttactgattgttgaaacttgtggtttttcag

Basic information

species Physcomitrella patens
transcript PP1S65_136V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S65_136V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA09G36870.1 (Glycine max), 5'ss of exon 4
ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttcttgggggtctgtcagaccaactgggcttgc--cacgtcaaggttatgttttgtta-----tttgt-cattgggaaaataacaagttttactgattgttgaaacttgtggtttttcag
||| || | ||||| |||||||||||||| || ||||||||||| || |||||  |||||||||| || || || | |||||  | |   ||    |||      ||   | |  ||||  || | ||   || | ||   | |     |  || | ||||  ||||    |    | || ||                       
ATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatgttctctgt---tcttcacctcccttttgttttgcttcatgacatacttttattcaatgaaaccttccgttcgttggagaaattgacaaccatgcttat-----------------------

upper sequence: PP1S65_136V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA09G36870.2 (Glycine max), 5'ss of exon 4
ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttcttgggggtctgtcagaccaactgggcttgc--cacgtcaaggttatgttttgtta-----tttgt-cattgggaaaataacaagttttactgattgttgaaacttgtggtttttcag
||| || | ||||| |||||||||||||| || ||||||||||| || |||||  |||||||||| || || || | |||||  | |   ||    |||      ||   | |  ||||  || | ||   || | ||   | |     |  || | ||||  ||||    |    | || || |||                   
ATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGGTATgttctctgt---tcttcacctcccttttgttttgcttcatgacatacttttattcaatgaaaccttccgttcgttggagaaattgacaaccatgcttat-gtta------------------

upper sequence: PP1S65_136V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: AT2G46280.3 (Arabidopsis thaliana), 5'ss of exon 6
ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttcttgggggtctgtca-gaccaactgggcttgccacgtcaaggttatgttttgt-tatttgtcattgggaaaataacaagttttactgattgttgaaacttgtggtttttcag
||| |  | || || ||||| |||||||| ||||| |||||||||||||||||  |||| || ||||| || || |  ||||    |         |   |   ||   | ||       |    || | | | ||||||  | | |||  ||||     | ||    |||   || |||  | | ||  |         
ATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAGgtaaattaacaacatttggattttgattgattgacacaatcctcacatgatgaggttttgagtgtgtgtt-ttggctctctcactgagtttgtggaatgt--atatttcag---------

upper sequence: PP1S65_136V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: Vv01s0011g06630.t01 (Vitis vinifera), 5'ss of exon 7
ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttcttgggggtctgtcagaccaactgggcttgccacgtcaaggttatgttttgttatttgtcattgggaaaataacaagttttactgattgttgaaacttgtggtttttcag
||| || | ||||| ||||| |||||||| || ||||||||||||||||||||  | || || || || || || |  |||| | |||  |     ||| | |   ||  ||   ||||    | ||| || |  |     |||  | |     |     |||  ||  | |    ||||||||              
ATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAGgtacactttct-----tctattatggca--tgttattgctg-attaagtttct--taaaacattgatgagcaaaagctccacattttcaaatttaggttgaaacaccctc--------

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:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|162169289|gb|FC345451.1|FC345451
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|162157953|gb|FC334406.1|FC334406
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|37837336|gb|BJ595344.1|BJ595344
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|162154178|gb|FC330621.1|FC330621
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|162169288|gb|FC345450.1|FC345450
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|162234376|gb|FC410122.1|FC410122
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|162183538|gb|FC359012.1|FC359012
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|37828721|gb|BJ586733.1|BJ586733
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|7286852|gb|AW599339.1|AW599339
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|208382679|gb|DC919833.1|DC919833
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|162191096|gb|FC367358.1|FC367358
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|162206922|gb|FC383499.1|FC383499
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|67699908|gb|BJ960141.1|BJ960141
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|162207651|gb|FC383528.1|FC383528
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|37823102|gb|BJ581168.1|BJ581168
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|67578003|gb|BJ950170.1|BJ950170
EST:     ATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: ATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|67723772|gb|BJ974031.1|BJ974031
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|162207650|gb|FC383527.1|FC383527
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|162262026|gb|FC437873.1|FC437873
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|37842238|gb|BJ600246.1|BJ600246
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATNCGTCCGTGTGCA
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCA
EST: gi|37834954|gb|BJ592966.1|BJ592966
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|18334496|gb|BJ166513.1|BJ166513
EST:     GGTCACCTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
EST: gi|37852444|gb|BJ610452.1|BJ610452
EST:     GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG                         TTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC
genomic: GGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGC

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: 33 (upstream exon), 35 (downstream exon)
Score: 19

ATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAGgtgcgcttct ... ggtttttcagTTTCTCAAGTGGCGGTGAGGATGGATACGTCCGTGTGCACTTCTTCGACGCTGACTACTACCACATCAAGGTTTAGGAAGTGTCTCTTCGCAAGTGGTAG




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