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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaacttaactttcaactagtttaacaggttccactatttttgtatgagtatttggtagcaacttgtctgataaacactgcttttacgctatcttgcagATCTGGACAAGTACTTTGAGAAGGACAGGTATCACTGCAAGGCACATCGATTGGTTTTCAAAA

Basic information

species Physcomitrella patens
transcript PP1S414_24V6.1
intron # 17
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|162258015|gb|FC434109.1|FC434109
EST:     AGCTGGCTGAATTTGTGAAGAGGCGGCTGAAGAACGAGACGACAGCTTCT                         ATCTGGACAAGTACTTTGAGAAGGACAGGTATCACTGCAAGGCACATCGAT
genomic: AGCTGGCTGAATTTGTGAAGAGGCGGCTGAAGAACGAGACGACAGCTTCTgtaataaact ... tatcttgcagATCTGGACAAGTACTTTGAGAAGGACAGGTATCACTGCAAGGCACATCGAT
EST: gi|37843086|gb|BJ601094.1|BJ601094
EST:     TGAAGAACGAGACGACAGCTTCT                         ATCTGGACAAGTACTTTGAGAAGGACAGGTATCACTGCAAGGCACATCGAT
genomic: TGAAGAACGAGACGACAGCTTCTgtaataaact ... tatcttgcagATCTGGACAAGTACTTTGAGAAGGACAGGTATCACTGCAAGGCACATCGAT
EST: gi|67698398|gb|BJ958631.1|BJ958631
EST:     GACGACAGCTTCT                         ATCTGGACAAGTACTTTGAGAAGGACAGGTATCACTGCAAGGCACATCGAT
genomic: GACGACAGCTTCTgtaataaact ... tatcttgcagATCTGGACAAGTACTTTGAGAAGGACAGGTATCACTGCAAGGCACATCGAT
EST: gi|208397007|gb|DC924685.1|DC924685
EST:     AGCTGGCTGNATTTGNGAAGAGGCGGCTGAAGAACGAGACGACAGCTTCT                         ATCTGGACAAGTACTTTGAGAAGGACAGGTATCACTGCAAGGCACATCGAT
genomic: AGCTGGCTGAATTTGTGAAGAGGCGGCTGAAGAACGAGACGACAGCTTCTgtaataaact ... tatcttgcagATCTGGACAAGTACTTTGAGAAGGACAGGTATCACTGCAAGGCACATCGAT

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), 23 (downstream exon)
Score: 2

TGAAGCTGGAGAAAAGTATGCACTCAAGCTGGCTGAATTTGTGAAGAGGCGGCTGAAGAACGAGACGACAGCTTCTgtaataaact ... tatcttgcagATCTGGACAAGTACTTTGAGAAGGACAGGTATCACTGCAAGGCACATCGATTGGTTTTCAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgagtatttggtagcaacttgtctgataaacactgcttttacgctatcttgcagATCTGGACAAGTACTTTGAGAAGGACAGGTATCACTGCAAGGCACATCGATTGGTTTTCAAAA
                     gtctgat  putative branch site (score: 2)
                                            ctatctt  putative PPT
                        tgataaa  TA-rich tract