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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcatgtagtatcaggttttgattgatagattttgagcattttgttacatatattagtatcgtgcacaagcaccggttaacatacgtttcttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGACCAACAAGCTTGACAGA

Basic information

species Physcomitrella patens
transcript PP1S299_37V6.1
intron # 5
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|37826425|gb|BJ584437.1|BJ584437
EST:     ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGG                         GCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
genomic: ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGGgtaaagtact ... cttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
EST: gi|208388439|gb|DC957049.1|DC957049
EST:     ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGG                         GCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
genomic: ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGGgtaaagtact ... cttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
EST: gi|208400674|gb|DC908971.1|DC908971
EST:     ATTGATAA-GTAACTTCAGGACAACGATTGGATTTAA-TCTANAGAGGGG                         -CGNAT-CNGGATGANCTTTCC-CTCA-TCTACA
genomic: ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGGgtaaagtact ... cttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACA
EST: gi|208351479|gb|DC921784.1|DC921784
EST:     ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGG                         GCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
genomic: ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGGgtaaagtact ... cttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
EST: gi|208356325|gb|DC957359.1|DC957359
EST:     ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGG                         GCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
genomic: ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGGgtaaagtact ... cttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
EST: gi|208358616|gb|DC949951.1|DC949951
EST:     ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGG                         GCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
genomic: ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGGgtaaagtact ... cttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
EST: gi|37832955|gb|BJ590967.1|BJ590967
EST:     ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGG                         GCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
genomic: ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGGgtaaagtact ... cttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
EST: gi|208378991|gb|DC922837.1|DC922837
EST:     ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGG                         GCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
genomic: ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGGgtaaagtact ... cttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
EST: gi|208370657|gb|DC936145.1|DC936145
EST:     ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGG                         GCGGATTCNGGATGAACTTTCCACTCANTCTACAGAAACGTCTAATTTGAC
genomic: ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGGgtaaagtact ... cttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
EST: gi|162208487|gb|FC384450.1|FC384450
EST:     ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGG                         GCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
genomic: ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGGgtaaagtact ... cttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
EST: gi|208345784|gb|DC921025.1|DC921025
EST:     ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGG                         GCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC
genomic: ATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGGgtaaagtact ... cttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGAC

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), 33 (downstream exon)
Score: 4

TTATGCGATTGATAAAGTAACTTCAGGACAACGATTGGATTTAAATCTAGAGAGGGGgtaaagtact ... cttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGACCAACAAGCTTGACAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatatattagtatcgtgcacaagcaccggttaacatacgtttcttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGACCAACAAGCTTGACAGA
                              ggttaac  putative branch site (score: 4)
                                        cgtttcttcct  putative PPT
     tatattagtat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcatgtagtatcaggttttgattgatagattttgagcattttgttacatatattagtatcgtgcacaagcaccggttaacatacgtttcttcctgcagGCGGATTCGGGATGAACTTTCCACTCAATCTACAGAAACGTCTAATTTGACCAACAAGCTTGACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaagc