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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcactcacagttgtcctcgacctcatctgtgtatattggcctatattgtccttcaagcatggttttgaacttctctggtacactgacaatttatctgacccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAATGCAGCCGATGCAAGACAAGCTGAATTAGACGCTACAAATACTAATCTAC

Basic information

species Physcomitrella patens
transcript PP1S129_53V6.1
intron # 14
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|162181747|gb|FC357346.1|FC357346
EST:     GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
EST: gi|162168328|gb|FC344642.1|FC344642
EST:     GCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
EST: gi|37844061|gb|BJ602069.1|BJ602069
EST:     GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
EST: gi|162268143|gb|FC443821.1|FC443821
EST:     GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
EST: gi|37841807|gb|BJ599815.1|BJ599815
EST:     GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
EST: gi|37849671|gb|BJ607679.1|BJ607679
EST:     GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
EST: gi|162168329|gb|FC344643.1|FC344643
EST:     GCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
EST: gi|162198683|gb|FC373464.1|FC373464
EST:     GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
EST: gi|162167515|gb|FC343699.1|FC343699
EST:     GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
EST: gi|162165626|gb|FC341465.1|FC341465
EST:     GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
EST: gi|208371453|gb|DC955789.1|DC955789
EST:     GGCGAAGCAACTGGGGGAAGGGCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
EST: gi|162165627|gb|FC341466.1|FC341466
EST:     GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
EST: gi|37827443|gb|BJ585455.1|BJ585455
EST:     GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
EST: gi|162198682|gb|FC373463.1|FC373463
EST:     GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGA                         GTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT
genomic: GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAAT

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), 23 (downstream exon)
Score: 7

GGCGAAGCAACTGGAGGAAGGGCCCCATGGGAAGGAgtaagcactc ... acccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAATGCAGCCGATGCAAGACAAGCTGAATTAGACGCTACAAATACTAATCTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaagcatggttttgaacttctctggtacactgacaatttatctgacccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAATGCAGCCGATGCAAGACAAGCTGAATTAGACGCTACAAATACTAATCTAC
                                              cccctgc  CT-rich tract
                                 acaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcactcacagttgtcctcgacctcatctgtgtatattggcctatattgtccttcaagcatggttttgaacttctctggtacactgacaatttatctgacccctgcagGTGCGAGCGAGATGCAGATACGAATGGGATGTTTACACAAAGCGGTGGAATGCAGCCGATGCAAGACAAGCTGAATTAGACGCTACAAATACTAATCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA