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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacggataaactgacttgaatcgatcataaagactgcctcgaaattgtgtagtgcgcaataaagattgagggattgacgtaccttgtgtgattgatgcagGTAGCTGCTTCTCTGGAGGTTTTGGTAAGACCCGTGGTATTGAAGACTATGCTACAGGTTCTAAGCCTTCTCAGTACAGGGTGGGGTACTGCTTTGCTTG

Basic information

species Physcomitrella patens
transcript PP1S48_250V6.1
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|100449535|gb|CJ973808.1|CJ973808
EST:     TCGCGAGGTTTTACGAAGCGAACGCTTCAGATGAGGGAGTAGCTGAAGTT                         GTAGCTGCTTCTCTGGAGGTTTTGGTAAGACCCGTGGTATTGAAGACTATG
genomic: TCGCGAGGTTTTACGAAGCGAACGCTTCAGATGAGGGAGTAGCTGAAGTTgtacgttttc ... attgatgcagGTAGCTGCTTCTCTGGAGGTTTTGGTAAGACCCGTGGTATTGAAGACTATG
EST: gi|162256707|gb|FC433225.1|FC433225
EST:     TCGCGAGGTTTTACGAAGCGAACGCTTCAGATGAGGGAGTAGCTGAAGTT                         GTAGCTGCTTCTCTGGAGGTTTTGGTAAGACCCGTGGTATTGAAGACTATG
genomic: TCGCGAGGTTTTACGAAGCGAACGCTTCAGATGAGGGAGTAGCTGAAGTTgtacgttttc ... attgatgcagGTAGCTGCTTCTCTGGAGGTTTTGGTAAGACCCGTGGTATTGAAGACTATG
EST: gi|18328101|gb|BJ160105.1|BJ160105
EST:     TCGCGAGGTTTTACGAAGCGAACGCTTCAGATGAGGGAGTAGCTGAAGTT                         GTAGCTGCTTCTCTGGAGGTTTTGGTAAGACCCGTGGTATTGAAGACTATG
genomic: TCGCGAGGTTTTACGAAGCGAACGCTTCAGATGAGGGAGTAGCTGAAGTTgtacgttttc ... attgatgcagGTAGCTGCTTCTCTGGAGGTTTTGGTAAGACCCGTGGTATTGAAGACTATG
EST: gi|100403065|gb|BY973489.1|BY973489
EST:     TCGCGAGGTTTTACGAAGCGAACGCTTCAGATGAGGGAGTAGCTGAAGTT                         GTAGCTGCTTCTCTGGAGGTTTTGGTAAGACCCGTGGTATTGAAGACTATG
genomic: TCGCGAGGTTTTACGAAGCGAACGCTTCAGATGAGGGAGTAGCTGAAGTTgtacgttttc ... attgatgcagGTAGCTGCTTCTCTGGAGGTTTTGGTAAGACCCGTGGTATTGAAGACTATG
EST: gi|18344379|gb|BJ176419.1|BJ176419
EST:     TCGCGAGGTTTTACGAAGCGAACGCTTCAGATGAGGGAGTAGCTGAAGTT                         GTAGCTGCTTCTCTGGAGGTTTTGGTAAGACCCGTGGTATTGAAGACTATG
genomic: TCGCGAGGTTTTACGAAGCGAACGCTTCAGATGAGGGAGTAGCTGAAGTTgtacgttttc ... attgatgcagGTAGCTGCTTCTCTGGAGGTTTTGGTAAGACCCGTGGTATTGAAGACTATG

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: 16 (upstream exon), 29 (downstream exon)
Score: 2

CAAAGACGGTGAAGCATTCGAGCTTATGCGAGGAGTGACGGCGGAGGATGTCGCGAGGTTTTACGAAGCGAACGCTTCAGATGAGGGAGTAGCTGAAGTTgtacgttttc ... attgatgcagGTAGCTGCTTCTCTGGAGGTTTTGGTAAGACCCGTGGTATTGAAGACTATGCTACAGGTTCTAAGCCTTCTCAGTACAGGGTGGGGTACTGCTTTGCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtagtgcgcaataaagattgagggattgacgtaccttgtgtgattgatgcagGTAGCTGCTTCTCTGGAGGTTTTGGTAAGACCCGTGGTATTGAAGACTATGCTACAGGTTCTAAGCCTTCTCAGTACAGGGTGGGGTACTGCTTTGCTTG
            aataaagatt  TA-rich tract