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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaccggttgaattactctctgttatttaatgcttgtttcggaatcagtggcacaacaatcgtgcatccatttcatgcgtataccttaacgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGACCTAAGGGAGGAGAAGTGGGCGTGCATGGCACTCGCAACAGGGTTGTAAA

Basic information

species Physcomitrella patens
transcript PP1S9_370V6.1
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

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|18367094|gb|BJ199174.1|BJ199174
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|67572154|gb|BJ944978.1|BJ944978
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|37847521|gb|BJ605529.1|BJ605529
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|162265591|gb|FC441073.1|FC441073
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|18372180|gb|BJ203782.1|BJ203782
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|162265590|gb|FC441072.1|FC441072
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|67695522|gb|BJ955755.1|BJ955755
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|162265967|gb|FC442970.1|FC442970
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|18368218|gb|BJ200303.1|BJ200303
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|18365284|gb|BJ197358.1|BJ197358
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|18334246|gb|BJ166262.1|BJ166262
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|18342795|gb|BJ174831.1|BJ174831
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|208353048|gb|DC921834.1|DC921834
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|37821939|gb|BJ580005.1|BJ580005
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
EST: gi|208397460|gb|DC916372.1|DC916372
EST:     TGCTATCATTCATTCTATTCTGGAC                         ATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC
genomic: TGCTATCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGAC

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), 27 (downstream exon)
Score: 7

TCATTCATTCTATTCTGGACgtatcctttg ... cgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGACCTAAGGGAGGAGAAGTGGGCGTGCATGGCACTCGCAACAGGGTTGTAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtggcacaacaatcgtgcatccatttcatgcgtataccttaacgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGACCTAAGGGAGGAGAAGTGGGCGTGCATGGCACTCGCAACAGGGTTGTAAA
                                     taccttaac  putative branch site 
                         atttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaccggttgaattactctctgttatttaatgcttgtttcggaatcagtggcacaacaatcgtgcatccatttcatgcgtataccttaacgttcaacagATTTGCATATGACATTGTACACATTTTTTAAGACCTGTTTTAGCGGTGGACCTAAGGGAGGAGAAGTGGGCGTGCATGGCACTCGCAACAGGGTTGTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT