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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctattcagttagtagtaaataaatgcactgttaaaccaatatgtagttgcagtttatcttgtgatcatttgccggaaaattcaacactctataggtgacatcctgtgatctaattggtttacttttgttttatttacagGGAAGAGATCAAGTAACTCCCATGTTACTGCAAAACCAAAGCGTGCAAGTAAACCGGGTGTCTTCAAAACCCTTATCGCTTGCTCAAAAGACTCTCAAAG

Basic information

species Physcomitrella patens
transcript PP1S94_54V6.1
intron # 2
splice site 3'
intron type U2

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: 21 (upstream exon), 15 (downstream exon)
Score: 1

CTCCCTTGTGCTAGTCCACGTTACTTGGCAATTTTTGAAGTTGATCATAGAAAAGCCGTCAGGAACCTAGTATTTAGTTATGTACACTTCGGCTTTCCATgtatcctatt ... ttatttacagGGAAGAGATCAAGTAACTCCCATGTTACTGCAAAACCAAAGCGTGCAAGTAAACCGGGTGTCTTCAAAACCCTTATCGCTTGCTCAAAAGACTCTCAAAG































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactctataggtgacatcctgtgatctaattggtttacttttgttttatttacagGGAAGAGATCAAGTAACTCCCATGTTACTGCAAAACCAAAGCGTGCAAGTAAACCGGGTGTCTTCAAAACCCTTATCGCTTGCTCAAAAGACTCTCAAAG
                       atctaat  putative branch site (score: 1)
                                 tttacttttgtttt  putative PPT
                                 tttacttttgttttat  TA-rich tract