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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagttcgtgccatgaaggttgaatcgatgcaggggagttagaaacaactgaaatgtggagaaagtgttaactggttacgatgttatatgatcttcgcagGTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGATGCCACGGCAACCGCGCCCTTGTTTTACCACACTGCTGAGGCTTCGACT

Basic information

species Physcomitrella patens
transcript PP1S48_203V6.2
intron # 2
splice site 3'
intron type U2

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|100359384|gb|BY965720.1|BY965720
EST:     CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTG                         GTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
genomic: CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTGgtaagcacta ... atcttcgcagGTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
EST: gi|100439351|gb|BY980220.1|BY980220
EST:     CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTG                         GTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
genomic: CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTGgtaagcacta ... atcttcgcagGTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
EST: gi|100383854|gb|BY987111.1|BY987111
EST:     CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTG                         GTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
genomic: CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTGgtaagcacta ... atcttcgcagGTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
EST: gi|100413133|gb|BY992603.1|BY992603
EST:     CTGACCTTCAGAGCCTATGACTGCAACGAACTGCCCAGTATGGAGAATTG                         GTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATACTGGATGTAGA
genomic: CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTGgtaagcacta ... atcttcgcagGTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
EST: gi|100355976|gb|BY946132.1|BY946132
EST:     CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTG                         GTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
genomic: CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTGgtaagcacta ... atcttcgcagGTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
EST: gi|18330210|gb|BJ162216.1|BJ162216
EST:     CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTG                         GTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
genomic: CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTGgtaagcacta ... atcttcgcagGTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
EST: gi|208373478|gb|DC941075.1|DC941075
EST:     CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTG                         GTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
genomic: CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTGgtaagcacta ... atcttcgcagGTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
EST: gi|208384905|gb|DC903412.1|DC903412
EST:     CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTG                         GTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
genomic: CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTGgtaagcacta ... atcttcgcagGTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
EST: gi|100417698|gb|BY975610.1|BY975610
EST:     CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTG                         GTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
genomic: CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTGgtaagcacta ... atcttcgcagGTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
EST: gi|100418558|gb|BY957478.1|BY957478
EST:     CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTG                         GTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA
genomic: CTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTGgtaagcacta ... atcttcgcagGTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGA

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), 31 (downstream exon)
Score: 10

TTGGAAGACGTCGAGTTAGTCGTGCTTCAAGCCTTTCATTGCAAATGAGTCTGACCTTCAGAGCCGATGACTGCAACGAACTGCCCAGTATGGAGAATTGgtaagcacta ... atcttcgcagGTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGATGCCACGGCAACCGCGCCCTTGTTTTACCACACTGCTGAGGCTTCGACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caactgaaatgtggagaaagtgttaactggttacgatgttatatgatcttcgcagGTTGAATGCGGGGGCAGACTGGAACGAGCATCATGGAATAGTGGATGTAGATGCCACGGCAACCGCGCCCTTGTTTTACCACACTGCTGAGGCTTCGACT
                    tgttaac  putative branch site (score: 10)
                                              tcttcgc  putative PPT
                                   atgttatat  TA-rich tract