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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctattgtgtgaaagtgcatagtgtgatagactggagagggattgcaatgtgataatacacgtgatatctgaggtgggtattgacttggcatttcgcagCCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCATTGTGCTATGAGGGGCGAAATCAAGCCT

Basic information

species Physcomitrella patens
transcript PP1S47_4V6.2
intron # 9
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|37850221|gb|BJ608229.1|BJ608229
EST:     TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAG                         CCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
genomic: TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAGgtatgtccct ... catttcgcagCCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
EST: gi|37837608|gb|BJ595616.1|BJ595616
EST:     TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAG                         CCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
genomic: TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAGgtatgtccct ... catttcgcagCCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
EST: gi|162242980|gb|FC417620.1|FC417620
EST:     TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAG                         CCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
genomic: TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAGgtatgtccct ... catttcgcagCCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
EST: gi|37833593|gb|BJ591605.1|BJ591605
EST:     TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAG                         CCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTAGGGCGTCCAT
genomic: TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAGgtatgtccct ... catttcgcagCCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
EST: gi|162241570|gb|FC414692.1|FC414692
EST:     TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAG                         CCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
genomic: TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAGgtatgtccct ... catttcgcagCCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
EST: gi|208358879|gb|DC957651.1|DC957651
EST:     TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAG                         CCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
genomic: TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAGgtatgtccct ... catttcgcagCCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
EST: gi|162241571|gb|FC414693.1|FC414693
EST:     TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAG                         CCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
genomic: TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAGgtatgtccct ... catttcgcagCCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
EST: gi|162248337|gb|FC422552.1|FC422552
EST:     TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAG                         CCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT
genomic: TAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAGgtatgtccct ... catttcgcagCCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCAT

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), 28 (downstream exon)
Score: 5

GAGGGGTCGGGATAAGACCTATTTCACGAGTGCATTCTCTGGGTACACAGTAGGCCTTCTAGTCACCATTTTGGTGATGAATTTGTTCCAGGCTGCACAGgtatgtccct ... catttcgcagCCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCATTGTGCTATGAGGGGCGAAATCAAGCCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatgtgataatacacgtgatatctgaggtgggtattgacttggcatttcgcagCCTGCACTTCTTTACATCGTACCGGGAGTGATCGGGTTTTTGGGCGTCCATTGTGCTATGAGGGGCGAAATCAAGCCT
                                  tattgac  putative branch site (score: 5)
      tgataata  TA-rich tract