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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagattctttcgacgaagcttgccctagacctttgttgatagccgaaactcgctgtgaacataggctctaaagtggtgctaatttcaagtgggtactcagGGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCCTTCAATCCCATCCAAGGATGCCCGTCCACAATACTCTTCAGCTGACGTA

Basic information

species Physcomitrella patens
transcript PP1S79_94V6.1
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|208359039|gb|DC957787.1|DC957787
EST:     ATCAAGTGCCTCGTGATTGAGGATGCTCC                         GGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCC
genomic: ATCAAGTGCCTCGTGATTGAGGATGCTCCgtaagctcca ... gggtactcagGGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCC
EST: gi|100384461|gb|BY987320.1|BY987320
EST:     AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGACGATGCTCC                         GGCTGGTGTATTGGCAGCTAAAGCTGCAGGAATGCAAGTGGTGGCAGTTCC
genomic: AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCCgtaagctcca ... gggtactcagGGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCC
EST: gi|18355214|gb|BJ187273.1|BJ187273
EST:     AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCC                         GGCTGGTGTATTGGCAGCTAA
genomic: AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCCgtaagctcca ... gggtactcagGGCTGGTGTATTGGCAGCTAA
EST: gi|100422965|gb|BY958088.1|BY958088
EST:     AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCC                         GGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCC
genomic: AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCCgtaagctcca ... gggtactcagGGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCC
EST: gi|162214903|gb|FC390463.1|FC390463
EST:     AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCC                         GGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCC
genomic: AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCCgtaagctcca ... gggtactcagGGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCC
EST: gi|100387881|gb|BY970626.1|BY970626
EST:     AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCC                         GGCTGGGGTATTGGCAGCTAAGGCTGCA
genomic: AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCCgtaagctcca ... gggtactcagGGCTGGTGTATTGGCAGCTAAGGCTGCA
EST: gi|100356058|gb|BY946175.1|BY946175
EST:     AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCC                         GGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCC
genomic: AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCCgtaagctcca ... gggtactcagGGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCC
EST: gi|208360015|gb|DC939319.1|DC939319
EST:     AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCC                         GGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCC
genomic: AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCCgtaagctcca ... gggtactcagGGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCC
EST: gi|208360201|gb|DC939198.1|DC939198
EST:     AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCC                         GGCTGGTGTATTGGCAGCTAANGCTGCANGAATGCAAGTGGTGGCAGTTCC
genomic: AGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCCgtaagctcca ... gggtactcagGGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCC

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: 34 (upstream exon), 34 (downstream exon)
Score: 5

ATTTCTAGAAGCCGCAAGCCGACTAAACGTGGAGCCAATCAAGTGCCTCGTGATTGAGGATGCTCCgtaagctcca ... gggtactcagGGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCCTTCAATCCCATCCAAGGATGCCCGTCCACAATACTCTTCAGCTGACGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactcgctgtgaacataggctctaaagtggtgctaatttcaagtgggtactcagGGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCCTTCAATCCCATCCAAGGATGCCCGTCCACAATACTCTTCAGCTGACGTA
                               tgctaat  putative branch site (score: 5)
                                  taatttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagattctttcgacgaagcttgccctagacctttgttgatagccgaaactcgctgtgaacataggctctaaagtggtgctaatttcaagtgggtactcagGGCTGGTGTATTGGCAGCTAAGGCTGCAGGAATGCAAGTGGTGGCAGTTCCTTCAATCCCATCCAAGGATGCCCGTCCACAATACTCTTCAGCTGACGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA