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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGAGCTGTGAGGGACGGGAAGAAATGGATCACATCGCCCATGGATGTTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAGgtgtggtgctgtgattggagtgttgatgaattcgacctttggggaatgaattagtttgttatgtttctgaggcacgtgatgccttgatggaattggaaga...

Basic information

species Physcomitrella patens
transcript PP1S400_36V6.1
intron # 2
splice site 5'
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|18364155|gb|BJ196228.1|BJ196228
EST:     TTGCGCGGGAAATCTCTCAGGGACTTACAAACAGCGCGCTCATTGCCGAG                         GTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
genomic: TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAGgtgtggtgct ... tagggcacagGTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
EST: gi|100389829|gb|BY971181.1|BY971181
EST:     TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAG                         GTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
genomic: TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAGgtgtggtgct ... tagggcacagGTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
EST: gi|18373215|gb|BJ204817.1|BJ204817
EST:     TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCGTTGCCGAG                         GTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
genomic: TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAGgtgtggtgct ... tagggcacagGTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
EST: gi|18375354|gb|BJ206932.1|BJ206932
EST:     TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAG                         GTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
genomic: TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAGgtgtggtgct ... tagggcacagGTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
EST: gi|18331447|gb|BJ163458.1|BJ163458
EST:     TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAG                         GTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
genomic: TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAGgtgtggtgct ... tagggcacagGTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
EST: gi|67572617|gb|BJ945441.1|BJ945441
EST:     TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAG                         GTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
genomic: TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAGgtgtggtgct ... tagggcacagGTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
EST: gi|18357116|gb|BJ189175.1|BJ189175
EST:     TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAG                         GTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
genomic: TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAGgtgtggtgct ... tagggcacagGTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
EST: gi|208391427|gb|DC937575.1|DC937575
EST:     TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAG                         GTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
genomic: TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAGgtgtggtgct ... tagggcacagGTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
EST: gi|67569369|gb|BJ942193.1|BJ942193
EST:     TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAG                         GTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT
genomic: TTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAGgtgtggtgct ... tagggcacagGTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACT

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), 31 (downstream exon)
Score: 6

GGATGGAGCTGTGAGGGACGGGAAGAAATGGATCACATCGCCCATGGATGTTGCGCGGGAAATCTCTCAGGGACTTGCAAACAGCGCGCTCATTGCCGAGgtgtggtgct ... tagggcacagGTGAATGGCGTGTTATGGGACATGACGAGACCATTGGAGGGCGACTGCACTCTACAGTTACACAAATTTGAGTCAGACAAGGGTCGCGACACCTTCTGGC




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