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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttgtgttttctgatattcatcaataaatagtgcttacaatcttgcgtagtgcttctaatggagtattgtgattttcttgtgtgaaccctcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG

Basic information

species Physcomitrella patens
transcript PP1S84_76V6.1
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|37851942|gb|BJ609950.1|BJ609950
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGCAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|208360945|gb|DC946634.1|DC946634
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|162182473|gb|FC357448.1|FC357448
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|18339266|gb|BJ171293.1|BJ171293
EST:     GATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: GATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|162258880|gb|FC434887.1|FC434887
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|208372438|gb|DC952282.1|DC952282
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|37847781|gb|BJ605789.1|BJ605789
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|208375291|gb|DC945018.1|DC945018
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|18334585|gb|BJ166602.1|BJ166602
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAATGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|208365784|gb|DC951047.1|DC951047
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|18334591|gb|BJ166608.1|BJ166608
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|208372580|gb|DC952357.1|DC952357
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|18340558|gb|BJ172586.1|BJ172586
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|162196646|gb|FC374936.1|FC374936
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|208367467|gb|DC955675.1|DC955675
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
EST: gi|37842276|gb|BJ600284.1|BJ600284
EST:     AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAG                         TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG
genomic: AGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGG

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: 26 (upstream exon), 34 (downstream exon)
Score: 19

GCTCTAGCTCAGTGTGAGCAAGGATTGACGAAGTTAGGTGTGGCTCGAGAAGCTGTAGATGATACTGCCGGAGCTGCACAGgtaatcgaaa ... tcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtagtgcttctaatggagtattgtgattttcttgtgtgaaccctcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG
         ttctaat  putative branch site (score: 19)
                                          ccctcgtct  putative PPT
                           attttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttgtgttttctgatattcatcaataaatagtgcttacaatcttgcgtagtgcttctaatggagtattgtgattttcttgtgtgaaccctcgtctgcagTTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA