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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttgacacaaattgacgttcttaatacaggacgtagggtttaaaagctgatgactgatgtcagatgagagcatgggtagtgctataaatgtgccagttttttctctcgagttgctcttcctgaaggtggatgatacatttatccttaagaattatttcagGGCGTTCGCAGTTTCTGGAGGCTGCACAAAGAGGTAACGTGGTGCCGGTATATCGGCGCATATTTTCCGATCATCTTACACCTGTGTTAGCATACCGATG

Basic information

species Physcomitrella patens
transcript PP1S77_252V6.1
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|100442715|gb|BY981540.1|BY981540
EST:     GCAGACAGCGGTAGATGTACCACCTTCTGAAGAACGAGAGACTACCCCAG                         GGCGTTCGCAGTTTCTGGAGGCTGCACAAAGAGGTAACGTGGTGCCGGTAT
genomic: GCAGACAGCGGTAGATGTACCACCTTCTGAAGAACGAGAGACTACCCCAGgtaatgttga ... attatttcagGGCGTTCGCAGTTTCTGGAGGCTGCACAAAGAGGTAACGTGGTGCCGGTAT
EST: gi|162171713|gb|FC348174.1|FC348174
EST:     TAGATGTACCACCTTCTGAAGAACGAGAGACTACCCCAG                         GGCGTTCGCAGTTTCTGGAGGCTGCACGAAGAGGTAACGTGGTGCCGGTAT
genomic: TAGATGTACCACCTTCTGAAGAACGAGAGACTACCCCAGgtaatgttga ... attatttcagGGCGTTCGCAGTTTCTGGAGGCTGCACAAAGAGGTAACGTGGTGCCGGTAT
EST: gi|100383453|gb|BY950237.1|BY950237
EST:     GCAGACAGCGGTAGATGTACCACCTTCTGAAGAACGAGAGACTACCCCAG                         GGCGTTCGCAGTTTCTGGAGGCTGCACAAAGAGGTAACGTGGTGCCGGTAT
genomic: GCAGACAGCGGTAGATGTACCACCTTCTGAAGAACGAGAGACTACCCCAGgtaatgttga ... attatttcagGGCGTTCGCAGTTTCTGGAGGCTGCACAAAGAGGTAACGTGGTGCCGGTAT
EST: gi|162167077|gb|FC342539.1|FC342539
EST:     GCAGACAGCGGTAGATGTACCACCTTCTGAAGAACGAGAGACTACCCCAG                         GGCGTTCGCAGTTTCTGGAGGCTGCACGAAGAGGTAACGTGGTGCCGGTAT
genomic: GCAGACAGCGGTAGATGTACCACCTTCTGAAGAACGAGAGACTACCCCAGgtaatgttga ... attatttcagGGCGTTCGCAGTTTCTGGAGGCTGCACAAAGAGGTAACGTGGTGCCGGTAT

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: 32 (upstream exon), 20 (downstream exon)
Score: 3

GGCGGTTGTGCCCGAGCATCGGTGAATCCTGTCATTTCCTGCACAGCTTTGCAGACAGCGGTAGATGTACCACCTTCTGAAGAACGAGAGACTACCCCAGgtaatgttga ... attatttcagGGCGTTCGCAGTTTCTGGAGGCTGCACAAAGAGGTAACGTGGTGCCGGTATATCGGCGCATATTTTCCGATCATCTTACACCTGTGTTAGCATACCGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgagttgctcttcctgaaggtggatgatacatttatccttaagaattatttcagGGCGTTCGCAGTTTCTGGAGGCTGCACAAAGAGGTAACGTGGTGCCGGTATATCGGCGCATATTTTCCGATCATCTTACACCTGTGTTAGCATACCGATG
                                              ttatttc  CT-rich tract
                               atttatccttaagaat  TA-rich tract