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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgtgcatttgtgtatcagaagtactttgatgaaattctgtcagttctaggtgaccgtattctgattcaagttaagtgtgtgtttctttgttttgcagCCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTTGATTACTTACTTGTAGTTGGCGTTGCCATAATCCTGAATGCAGCCAACA

Basic information

species Physcomitrella patens
transcript PP1S115_65V6.1
intron # 4
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|162243121|gb|FC416721.1|FC416721
EST:     CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACA                         CCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT
genomic: CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACAgtgagtttct ... tgttttgcagCCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT
EST: gi|208353226|gb|DC926151.1|DC926151
EST:     CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACA                         CCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT
genomic: CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACAgtgagtttct ... tgttttgcagCCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT
EST: gi|162243120|gb|FC416720.1|FC416720
EST:     CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACA                         CCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT
genomic: CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACAgtgagtttct ... tgttttgcagCCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT
EST: gi|162270236|gb|FC447248.1|FC447248
EST:     CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACA                         CCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT
genomic: CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACAgtgagtttct ... tgttttgcagCCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT
EST: gi|162218820|gb|FC394363.1|FC394363
EST:     CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACA                         CCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT
genomic: CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACAgtgagtttct ... tgttttgcagCCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT
EST: gi|162218819|gb|FC394362.1|FC394362
EST:     CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACA                         CCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT
genomic: CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACAgtgagtttct ... tgttttgcagCCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT
EST: gi|162270235|gb|FC447247.1|FC447247
EST:     CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACA                         CCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT
genomic: CATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACAgtgagtttct ... tgttttgcagCCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTT

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: 28 (upstream exon), 28 (downstream exon)
Score: 2

ACTTTAGAGACATTGAACAAGAAGGATGCTTGGCTGTTTTGGTGGACGTTGTATCTCACAgtgagtttct ... tgttttgcagCCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTTGATTACTTACTTGTAGTTGGCGTTGCCATAATCCTGAATGCAGCCAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctaggtgaccgtattctgattcaagttaagtgtgtgtttctttgttttgcagCCTATGGTGTGGGTGGCGCTTGGTATAGTTGCTGTGATCAAGTTCAACTTTGATTACTTACTTGTAGTTGGCGTTGCCATAATCCTGAATGCAGCCAACA
                ttctgat  putative branch site (score: 2)
                                     tgtttctttgtttt  putative PPT
                                           tttgtttt  TA-rich tract