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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggagtaatttcgatgcggcttcatttgctggtactgttgcggttgatgtggagaaagctgctggactcacttatcgtgacctcatatttcctcattgcagGTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACAAAGAGTATACGGATCCCCGCCGCGTGACAAAAACCGCTGCAATGAGTGC

Basic information

species Physcomitrella patens
transcript PP1S87_157V6.2
intron # 10
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|162238720|gb|FC418225.1|FC418225
EST:     AGCTTCTGGTCAGAGGAACACATACTCTCAGAACTCTAAATCTCTAGATG                         GTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACA
genomic: AGCTTCTGGTCAGAGGAACACATACTCTCAGAACTCTAAATCTCTAGATGgtaactacaa ... ctcattgcagGTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACA
EST: gi|162175518|gb|FC351768.1|FC351768
EST:     GTCAGAGGAACACATACTCTCAGAACTCTAAATCTCTAGATG                         GTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACA
genomic: GTCAGAGGAACACATACTCTCAGAACTCTAAATCTCTAGATGgtaactacaa ... ctcattgcagGTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACA
EST: gi|208392138|gb|DC957245.1|DC957245
EST:     AGCTTCTGGTCAGAGGAACACATACTCTCAGAACTCTAAATCTCTAGATG                         GTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACA
genomic: AGCTTCTGGTCAGAGGAACACATACTCTCAGAACTCTAAATCTCTAGATGgtaactacaa ... ctcattgcagGTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACA
EST: gi|37824784|gb|BJ582850.1|BJ582850
EST:     AATCTCTAGATG                         GTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACA
genomic: AATCTCTAGATGgtaactacaa ... ctcattgcagGTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACA
EST: gi|162175519|gb|FC351769.1|FC351769
EST:     AGCTTCTGGTCAGAGGAACACATACTCTCAGAACTCTAAATCTCTAGATG                         GTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACA
genomic: AGCTTCTGGTCAGAGGAACACATACTCTCAGAACTCTAAATCTCTAGATGgtaactacaa ... ctcattgcagGTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACA
EST: gi|18350707|gb|BJ182758.1|BJ182758
EST:     AGCTTCTGGTCAGAGGAACACATACTCTCAGAACTCTAAATCTCTAGATG                         GTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACA
genomic: AGCTTCTGGTCAGAGGAACACATACTCTCAGAACTCTAAATCTCTAGATGgtaactacaa ... ctcattgcagGTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACA

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), 34 (downstream exon)
Score: 10

GAAGCCGCGAAGTATCAAAGAGAGGAAAGTAAGTTGCAGGACAAGCATGGAGCTTCTGGTCAGAGGAACACATACTCTCAGAACTCTAAATCTCTAGATGgtaactacaa ... ctcattgcagGTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACAAAGAGTATACGGATCCCCGCCGCGTGACAAAAACCGCTGCAATGAGTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtggagaaagctgctggactcacttatcgtgacctcatatttcctcattgcagGTCCTGTTGGAAGAGCAGGTAATCCAACAAGTTTCATGGGCCTTTCCAACAAAGAGTATACGGATCCCCGCCGCGTGACAAAAACCGCTGCAATGAGTGC
                  gactcac  putative branch site (score: 10)
                                  cctcatatttcctc  putative PPT
                                    tcatattt  TA-rich tract