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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatattcaaacgttggtgacagttttggtttggaatgggatgtagtagatgatgtcatgggtgtcgtctcactggctggttgtgattgatgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTATTTCTGGTCACCATTCATTTTCC

Basic information

species Physcomitrella patens
transcript PP1S69_142V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S69_142V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ11261 (Selaginella moellendorffii), 3'ss of exon 1
gcatattcaaacgttggtgacagttttg-gtttggaatgggatgtagtagatgatgtcatgggtgtcgtctcactggctggttgtgattgatgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTATTTCTGGTCACCATTCATTTTCC
            ||  | | | | |    ||| |  ||   | |   ||  |||||  ||||      |||| |||           ||  | |    |||| ||||| || |||||||||||||| ||||| || ||||| ||||||||||| |||||||| || ||||| || || || ||||| ||||| || || ||
------------gtaagcggccgatcgatgttcgcgattctagggtttatgtgatggaatggaaaatttctc-ctg-----------ttcttctctcccagGGCCTGTCGCGGAGGATATGTTCCACTGGCAAGCGACGATCATGGGACCTCCCGATAGTCCCTACGCGGGTGGGGTTTTCCTGGTGACCATCCACTTCCC

upper sequence: PP1S69_142V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ15547 (Selaginella moellendorffii), 3'ss of exon 1
gcatattcaaacgttggtg-acagttttggtttggaatgggatgtagtagatgatgtcatgggtgtcgtctcactggctggttgtgattgatgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTATTTCTGGTCACCATTCATTTTCC
            ||  | | ||  |     || |  ||   | |   ||  |||||   |||      |||| |||           ||  | |    |||| ||||| || |||||||||||||| ||||| || ||||| ||||||||||| |||||||| || ||||| || || || ||||| ||||| || || ||
------------gtaagcggacgatcgatcttcgcgattctagggtttatgtgatggagtggaaaatttctc-ctg-----------ttcttctctcccagGGCCTGTCGCGGAGGATATGTTCCACTGGCAAGCGACGATCATGGGACCTCCCGATAGTCCCTACGCGGGTGGGGTTTTCCTGGTGACCATCCACTTCCC
















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|208400830|gb|DC925110.1|DC925110
EST:     GAAGGAG-TGAAAGATTTGCAGAA-GATTCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|67693812|gb|BJ954045.1|BJ954045
EST:     GCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|67570529|gb|BJ943353.1|BJ943353
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCT
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCT
EST: gi|67698111|gb|BJ958344.1|BJ958344
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|37852533|gb|BJ610541.1|BJ610541
EST:     ACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: ACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|162259705|gb|FC436724.1|FC436724
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|100355061|gb|BY964981.1|BY964981
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|208392747|gb|DC953644.1|DC953644
EST:     TTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: TTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|162272755|gb|FC448771.1|FC448771
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|67698855|gb|BJ959088.1|BJ959088
EST:     GAAGGAGTTGAAAGA-TTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|162232470|gb|FC408865.1|FC408865
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|67575390|gb|BJ948214.1|BJ948214
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|67507966|gb|BJ940840.1|BJ940840
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|100352295|gb|BY983136.1|BY983136
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|208395907|gb|DC911888.1|DC911888
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTNCATTGGCAGGCTACGATTATNGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|208355817|gb|DC930180.1|DC930180
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|67575658|gb|BJ948482.1|BJ948482
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|18359128|gb|BJ191188.1|BJ191188
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|162232471|gb|FC408866.1|FC408866
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|67694209|gb|BJ954442.1|BJ954442
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|208373983|gb|DC944716.1|DC944716
EST:     GAAGGAG-TGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|100358402|gb|BY983887.1|BY983887
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|67570907|gb|BJ943731.1|BJ943731
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|18351176|gb|BJ183227.1|BJ183227
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|162259704|gb|FC436723.1|FC436723
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|100403465|gb|BY991213.1|BY991213
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|18348205|gb|BJ180252.1|BJ180252
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|67569246|gb|BJ942070.1|BJ942070
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|67574694|gb|BJ947518.1|BJ947518
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|208373004|gb|DC940635.1|DC940635
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|67692502|gb|BJ952735.1|BJ952735
EST:     GAAGGAG-TGAAAGA-TTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
EST: gi|208384213|gb|DC911307.1|DC911307
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTG                         GACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTC

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), 31 (downstream exon)
Score: 7

TAGCGGTGTGCTGGTGGGTGGCTGCGTCTGATGGCCTCCAAGCGTATTCTGAAGGAGTTGAAAGATTTGCAGAAGGATCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGACCTGTGGCCGAGGATATGTTCCATTGGCAGGCTACGATTATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTATTTCTGGTCACCATTCATTTTCC




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