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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgacattggctggagcagtcttgcctagatatttttatgaagttctgatatgagtcctacattcttgctgttggattgagcttttcggcgagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTGGCAACTTTACTTCCTGCCAAGGCCAACG

Basic information

species Physcomitrella patens
transcript PP1S89_217V6.1
intron # 2
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|208387294|gb|DC933045.1|DC933045
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTATAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
EST: gi|208380398|gb|DC907723.1|DC907723
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
EST: gi|67578479|gb|BJ950646.1|BJ950646
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
EST: gi|100360402|gb|BY984109.1|BY984109
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
EST: gi|100421646|gb|BY976247.1|BY976247
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
EST: gi|100410182|gb|BY974451.1|BY974451
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
EST: gi|208379652|gb|DC903707.1|DC903707
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
EST: gi|100441473|gb|BY980895.1|BY980895
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
EST: gi|100410153|gb|BY974437.1|BY974437
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
EST: gi|100444813|gb|BY982641.1|BY982641
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
EST: gi|208371674|gb|DC932503.1|DC932503
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
EST: gi|100388937|gb|BY988813.1|BY988813
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
EST: gi|208351804|gb|DC910358.1|DC910358
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
EST: gi|100445691|gb|CJ969990.1|CJ969990
EST:     TGAGCTCCGCCAGTGAGAAGGATGATATCGACCAACAAACGACTGATAAG                         CTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG
genomic: TGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTG

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), 35 (downstream exon)
Score: 36

CAAGCAGGCTGTCACCCACGTCAATACTTTGAAGAAACTTCAAGGAGACGTGAGCTCCGCCAGTGAGAAGGATGATATCAACCAACAAACGACTGATAAGgttttcttca ... gagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTGGCAACTTTACTTCCTGCCAAGGCCAACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatatgagtcctacattcttgctgttggattgagcttttcggcgagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTGGCAACTTTACTTCCTGCCAAGGCCAACG
 ttctgat  putative branch site (score: 36)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgacattggctggagcagtcttgcctagatatttttatgaagttctgatatgagtcctacattcttgctgttggattgagcttttcggcgagtgtgcagCTGGAGGAGGAACTTTACAAAGCACGGACTATGCTTTACGATGGAGACGTGGCAACTTTACTTCCTGCCAAGGCCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA