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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttctgtcgggtatttgcccgagtgtgcgattcttttgggtgagttggatagagccttttagtatgtgctggtgattcgccggtctcttctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGCGTGCTGTACACCACTAA

Basic information

species Physcomitrella patens
transcript PP1S427_21V6.1
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|100378256|gb|BY949759.1|BY949759
EST:     TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
EST: gi|100408118|gb|BY955912.1|BY955912
EST:     TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
EST: gi|100363190|gb|BY984402.1|BY984402
EST:     TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
EST: gi|100395111|gb|BY953605.1|BY953605
EST:     TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
EST: gi|208360750|gb|DC930519.1|DC930519
EST:     GGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: GGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
EST: gi|208391118|gb|DC942058.1|DC942058
EST:     TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
EST: gi|100363057|gb|BY984335.1|BY984335
EST:     AGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: AGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
EST: gi|18358298|gb|BJ190357.1|BJ190357
EST:     TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
EST: gi|67709474|gb|BJ965290.1|BJ965290
EST:     TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
EST: gi|67573631|gb|BJ946455.1|BJ946455
EST:     TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
EST: gi|100423015|gb|BY958113.1|BY958113
EST:     TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
EST: gi|100444384|gb|BY982413.1|BY982413
EST:     TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
EST: gi|208390131|gb|DC941952.1|DC941952
EST:     TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: TTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
EST: gi|208356385|gb|DC934403.1|DC934403
EST:     GCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATG                         ACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC
genomic: GCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGC

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), 34 (downstream exon)
Score: 14

TTCAGGCAGGGTACACGCGGGTTGAAAGTAGCAGGAGATGGAAGTGAGGCTTGGCATTGGGCTCGCAGCATTTGCAGGAGGATGGGTGCTGCGCGTCATGgtacgtcgaa ... tctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGCGTGCTGTACACCACTAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggatagagccttttagtatgtgctggtgattcgccggtctcttctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGCGTGCTGTACACCACTAA
                                    ccggtctcttctctt  CT-rich tract
             ttttagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacttctgtcgggtatttgcccgagtgtgcgattcttttgggtgagttggatagagccttttagtatgtgctggtgattcgccggtctcttctcttgcagACATTTCTCGAGTAGCTGCACGCGGTGGAGACCCGGAGGCGTGTTACAGGCGTGCTGTACACCACTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA