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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccttattcatggttgtcgacatggttggtggaaacgaagttttgacattctattatttgtatgccttctgatatctgtcattttgtcattcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGGATCTGTTTCGACGCACGTGATCATAGTGTTGCTGCGGTCGCCCCAGATA

Basic information

species Physcomitrella patens
transcript PP1S75_75V6.1
intron # 1
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|100385252|gb|BY950844.1|BY950844
EST:     CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCG                         GAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
genomic: CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
EST: gi|100405645|gb|BY973781.1|BY973781
EST:     CTCGTGGTGCAGGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCG                         GAATTTGCTGACATTCCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
genomic: CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
EST: gi|100391857|gb|BY989582.1|BY989582
EST:     CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCG                         GAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
genomic: CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
EST: gi|100368601|gb|BY967087.1|BY967087
EST:     CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGTTCG                         GAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
genomic: CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
EST: gi|100384956|gb|BY969691.1|BY969691
EST:     CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCG                         GAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
genomic: CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
EST: gi|100351968|gb|BY964638.1|BY964638
EST:     CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCG                         GAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
genomic: CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
EST: gi|100411132|gb|BY956337.1|BY956337
EST:     CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCG                         GAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
genomic: CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
EST: gi|100354570|gb|BY983455.1|BY983455
EST:     CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCG                         GAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
genomic: CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
EST: gi|100391464|gb|BY971670.1|BY971670
EST:     CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCG                         GAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
genomic: CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
EST: gi|208363881|gb|DC943338.1|DC943338
EST:     CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCG                         GAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
genomic: CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
EST: gi|100441883|gb|BY981106.1|BY981106
EST:     CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCG                         GAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
genomic: CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
EST: gi|100395894|gb|BY972180.1|BY972180
EST:     CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCG                         GAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
genomic: CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
EST: gi|100353584|gb|BY964880.1|BY964880
EST:     CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCG                         GAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG
genomic: CTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGG

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: 5

CATACGGTCCTCCGCATCGCACTGATAATCCGGTCCGGTATTACCAAGTTCTCGTGGTGCATGCTCCAACGGCGTCACTGCTCGCCAAGGAATGAGCTCGgtgagtaatg ... tcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGGATCTGTTTCGACGCACGTGATCATAGTGTTGCTGCGGTCGCCCCAGATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattctattatttgtatgccttctgatatctgtcattttgtcattcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGGATCTGTTTCGACGCACGTGATCATAGTGTTGCTGCGGTCGCCCCAGATA
                     ttctgat  putative branch site (score: 5)
      tattatttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccttattcatggttgtcgacatggttggtggaaacgaagttttgacattctattatttgtatgccttctgatatctgtcattttgtcattcaattgcagGAATTTGCTGACATTTCTATCAGTGCTGGGACTCAATCAAGTGGTCATCGGATCTGTTTCGACGCACGTGATCATAGTGTTGCTGCGGTCGCCCCAGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC