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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaattctgagtcagttcagatgacatcacaattttgggacctgaaattggaccggaaaatcatgtgctgaccatcttgtgatgacgtttctggtgcagGGTGATCCATTGGAGTGGGTAAGCTCACATCGGTATCACCACCAGCATTGTGACACAGAGAAAGATCCACATTCTCCTTATGAAGGTTTCTGGCACAGTC

Basic information

species Physcomitrella patens
transcript PP1S495_13V6.1
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|100362419|gb|BY947347.1|BY947347
EST:     C-AAGTGGTTGGAGTACTCTTTCGCGTATTGTGGAGTCCAAGCGGTCCAG                         GGTGATCCATTGAAGTGGGTAAGCTCACATCGGTATCACC
genomic: CCAAGTGGTTGGAGTACTCTTTCGCGTATTGTGGAGTCCAAGCGGTCCAGgtttgtttta ... tctggtgcagGGTGATCCATTGGAGTGGGTAAGCTCACATCGGTATCACC
EST: gi|162231669|gb|FC408262.1|FC408262
EST:     CCAAGTGGTTGGAGTACTCTTTCGCGTATTGTGGAGTCCAAGCGGTCCAG                         GGTGATCCATTGGAGTGGGTAAGCTCACATCGGTATCACCACCAGCATTGT
genomic: CCAAGTGGTTGGAGTACTCTTTCGCGTATTGTGGAGTCCAAGCGGTCCAGgtttgtttta ... tctggtgcagGGTGATCCATTGGAGTGGGTAAGCTCACATCGGTATCACCACCAGCATTGT
EST: gi|162171757|gb|FC348426.1|FC348426
EST:     CCAAGTGGTTGGAGTACTCTTTCGCGTATTGTGGAGTCCAAGCGGTCCAG                         GGTGATCCATTGGAGTGGGTAAGCTCACATCGGTATCACCACCAGCATTGT
genomic: CCAAGTGGTTGGAGTACTCTTTCGCGTATTGTGGAGTCCAAGCGGTCCAGgtttgtttta ... tctggtgcagGGTGATCCATTGGAGTGGGTAAGCTCACATCGGTATCACCACCAGCATTGT
EST: gi|208388169|gb|DC941752.1|DC941752
EST:     CCAAGTGGTTGGAGTACTCTTTCNCGTATTGTGGANTCCAANCNGTCCAG                         GGTGATCCATNGGANTGGGTAANCTCACATCNGTATC
genomic: CCAAGTGGTTGGAGTACTCTTTCGCGTATTGTGGAGTCCAAGCGGTCCAGgtttgtttta ... tctggtgcagGGTGATCCATTGGAGTGGGTAAGCTCACATCGGTATC
EST: gi|22133439|gb|BQ827736.1|BQ827736
EST:     CCAAGTGGTTGGAGTACTCTTTCGCGTATTGTGGAGTCCAAGCGGTCCAG                         GGTGATCCATTGGAGTGGGTAAGCTCACATCGGTATCACCACCAGCATTGT
genomic: CCAAGTGGTTGGAGTACTCTTTCGCGTATTGTGGAGTCCAAGCGGTCCAGgtttgtttta ... tctggtgcagGGTGATCCATTGGAGTGGGTAAGCTCACATCGGTATCACCACCAGCATTGT

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), 35 (downstream exon)
Score: 7

GATCACGCTCTCCTTCCATCGCAATCTGTCACACAAAAGCTTCAAGCTCCCCAAGTGGTTGGAGTACTCTTTCGCGTATTGTGGAGTCCAAGCGGTCCAGgtttgtttta ... tctggtgcagGGTGATCCATTGGAGTGGGTAAGCTCACATCGGTATCACCACCAGCATTGTGACACAGAGAAAGATCCACATTCTCCTTATGAAGGTTTCTGGCACAGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattggaccggaaaatcatgtgctgaccatcttgtgatgacgtttctggtgcagGGTGATCCATTGGAGTGGGTAAGCTCACATCGGTATCACCACCAGCATTGTGACACAGAGAAAGATCCACATTCTCCTTATGAAGGTTTCTGGCACAGTC
                     tgctgac  putative branch site (score: 7)
                                         cgtttct  putative PPT
            aaaatcat  TA-rich tract