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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctccttgtcgattagttttaagctttcgcatgttggatgggaatttgcgcaatgggctttcggagctgactgtgagtgggtgttgggcacaatgtacagGGAACTGCGGAGAAATTCAGCATTGTGAGGTACTGCCTCTTCGCTTCTCCGGTGCATTTTCTATCGCTACTTTTCCACCTTCCCAAGTTCAATGACGAGA

Basic information

species Physcomitrella patens
transcript PP1S93_74V6.1
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|100438886|gb|BY961853.1|BY961853
EST:     GCGGACCTCCAGTTTGCATCGTGTCCGACATGTTCATGGGATTCACCCAG                         GGAACTGCGGAGAAATTCAGCATTGTGAGGTACTGCCTCTTCGCTTCTCCG
genomic: GCGGACCTCCAGTTTGCATCGTGTCCGACATGTTCATGGGATTCACCCAGgtcagttctg ... caatgtacagGGAACTGCGGAGAAATTCAGCATTGTGAGGTACTGCCTCTTCGCTTCTCCG
EST: gi|100384276|gb|BY969407.1|BY969407
EST:     GCGGACCTCCAGTTTGCATCGTGTCCGACATGTTCATGGGATTCACCCAG                         GGAACTGCGGANGAA-TTCAGCATTGTGAGGTACTGCCTCTTCGCTTTCTC
genomic: GCGGACCTCCAGTTTGCATCGTGTCCGACATGTTCATGGGATTCACCCAGgtcagttctg ... caatgtacagGGAACTGCGGA-GAAATTCAGCATTGTGAGGTACTGCCTCTTCGCTT-CTC
EST: gi|100446610|gb|CJ970909.1|CJ970909
EST:     GCGGACCTCCAGTTTGCATCGTGTCCGACATGTTCATGGGATTCACCCAG                         GGAACTGCGGAGAAATTCAGCATTGTGAGGTACTGCCTCTTCGCTTCTCCG
genomic: GCGGACCTCCAGTTTGCATCGTGTCCGACATGTTCATGGGATTCACCCAGgtcagttctg ... caatgtacagGGAACTGCGGAGAAATTCAGCATTGTGAGGTACTGCCTCTTCGCTTCTCCG

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-Seq library.


Block sizes: 34 (upstream exon), 35 (downstream exon)
Score: 29

CCATTACATTGAGGAGTCGCGGTCCATCAAGTATCCCAGCCGCTCCTCTAGCGGACCTCCAGTTTGCATCGTGTCCGACATGTTCATGGGATTCACCCAGgtcagttctg ... caatgtacagGGAACTGCGGAGAAATTCAGCATTGTGAGGTACTGCCTCTTCGCTTCTCCGGTGCATTTTCTATCGCTACTTTTCCACCTTCCCAAGTTCAATGACGAGA































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcgcaatgggctttcggagctgactgtgagtgggtgttgggcacaatgtacagGGAACTGCGGAGAAATTCAGCATTGTGAGGTACTGCCTCTTCGCTTCTCCGGTGCATTTTCTATCGCTACTTTTCCACCTTCCCAAGTTCAATGACGAGA
                   agctgac  putative branch site (score: 29)