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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttaaggtcgtgctttttgtcgcttaccaaggagtgtgaagaatctaatctctctcctgaaattgcattaactcaagaagactgttgtttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATTACTGCGGTCATGACAGAGGTTCTGAATGATAGCCTGGAGAACGTAGGCC

Basic information

species Physcomitrella patens
transcript PP1S299_37V6.1
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|208388439|gb|DC957049.1|DC957049
EST:     CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
EST: gi|208400674|gb|DC908971.1|DC908971
EST:     CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
EST: gi|208376965|gb|DC936771.1|DC936771
EST:     CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
EST: gi|208356325|gb|DC957359.1|DC957359
EST:     CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
EST: gi|208384733|gb|DC907150.1|DC907150
EST:     CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
EST: gi|208378991|gb|DC922837.1|DC922837
EST:     CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
EST: gi|100358057|gb|BY965450.1|BY965450
EST:     CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
EST: gi|100384951|gb|BY969686.1|BY969686
EST:     CTGTGGTTCCCAAGGGCAAGAGGCTCTNTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
EST: gi|208370657|gb|DC936145.1|DC936145
EST:     CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
EST: gi|18356011|gb|BJ188070.1|BJ188070
EST:     CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
EST: gi|208345784|gb|DC921025.1|DC921025
EST:     CTGTGGGTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
EST: gi|100447337|gb|CJ971636.1|CJ971636
EST:     CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
EST: gi|208386416|gb|DC937083.1|DC937083
EST:     CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
EST: gi|208392391|gb|DC907896.1|DC907896
EST:     CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTG                         GTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT
genomic: CTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATT

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), 33 (downstream exon)
Score: 3

ATTCTTTCCACGGGCATGGAGTCATGTCTATTCACAGAATGCTTCGCAAGCTGTGGTTCCCAAGGGCAAGAGGCTCTTTCTTGTGGATACCCTAGCTCTGgtaatgtcat ... ttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATTACTGCGGTCATGACAGAGGTTCTGAATGATAGCCTGGAGAACGTAGGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaatctctctcctgaaattgcattaactcaagaagactgttgtttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATTACTGCGGTCATGACAGAGGTTCTGAATGATAGCCTGGAGAACGTAGGCC
                      cattaac  putative branch site (score: 3)
                                         ttgttttttt  putative PPT
                                         ttgttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttaaggtcgtgctttttgtcgcttaccaaggagtgtgaagaatctaatctctctcctgaaattgcattaactcaagaagactgttgtttttttacagGTGAGAAGGCTAGAGTCGCAGGGCATGACGCCAAAGCAGTCGGAAGCTATTACTGCGGTCATGACAGAGGTTCTGAATGATAGCCTGGAGAACGTAGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA