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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgttttatcacattaccgctggtgcaactggtagtttcgtggatgcgtgctggtcttgatggagattgataggcatgtccttcggttgaagtgaggagaaaccttacttaagtttctcaaacactttgcagGAGCACTACGGGGAATTAAAGGAGAAACCATTTTACGGAAAGCTCGTTGCCTACATCATATCAGGCCCTGTCGTGTGCATT

Basic information

species Physcomitrella patens
transcript PP1S56_113V6.1
intron # 3
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|208345740|gb|DC909671.1|DC909671
EST:     TTCAGCTCATAGGATTGAAGCTGTTCAAAACCCCTAAAGAGCTTGCAGAG                         GAGCACTACGGGGAATTAAAGGAGAAACCATTTTACGGAAAGCTCGTTGCC
genomic: TTCAGCTCATAGGATTGAAGCTGTTCAAAACCCCTAAAGAGCTTGCAGAGgtgagcgttt ... cactttgcagGAGCACTACGGGGAATTAAAGGAGAAACCATTTTACGGAAAGCTCGTTGCC
EST: gi|162230181|gb|FC406329.1|FC406329
EST:     TTCAGCTCATAGGATTGAAGCTGTTCAAAACCCCTAAAGAGCTTGCAGAG                         GAGCACTACGGGGAATTAAAGGAGAAACCATTTTACGGAAAGCTCGTTGCC
genomic: TTCAGCTCATAGGATTGAAGCTGTTCAAAACCCCTAAAGAGCTTGCAGAGgtgagcgttt ... cactttgcagGAGCACTACGGGGAATTAAAGGAGAAACCATTTTACGGAAAGCTCGTTGCC
EST: gi|162216270|gb|FC392687.1|FC392687
EST:     TTCAGCTCATAGGATTGAAGCTGTTCAAAACCCCTAAAGAGCTTGCAGAG                         GAGCACTACGGGGAATTAAAGGAGAAACCATTTTACGGAAAGCTCGTTGCC
genomic: TTCAGCTCATAGGATTGAAGCTGTTCAAAACCCCTAAAGAGCTTGCAGAGgtgagcgttt ... cactttgcagGAGCACTACGGGGAATTAAAGGAGAAACCATTTTACGGAAAGCTCGTTGCC

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: 27 (upstream exon), 35 (downstream exon)
Score: 4

GTAGGTGAGATAATCTCTAGGTTTGAGCGGAAAGGCTTTCAGCTCATAGGATTGAAGCTGTTCAAAACCCCTAAAGAGCTTGCAGAGgtgagcgttt ... cactttgcagGAGCACTACGGGGAATTAAAGGAGAAACCATTTTACGGAAAGCTCGTTGCCTACATCATATCAGGCCCTGTCGTGTGCATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccttcggttgaagtgaggagaaaccttacttaagtttctcaaacactttgcagGAGCACTACGGGGAATTAAAGGAGAAACCATTTTACGGAAAGCTCGTTGCCTACATCATATCAGGCCCTGTCGTGTGCATT
                        accttac  putative branch site (score: 4)
                           ttacttaa  TA-rich tract