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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgggtacctgtgcgggagtgttcaggtgtgttagactagtcaaattcgcacaaatcattcgcgatatttgaagactcaccacaaggattcttttttgcagACAAATGTGGGAACTGTGGATGCGCATGTTGCAGACTATCAGCAAATGATAGACAATCTTCAA

Basic information

species Physcomitrella patens
transcript PP1S7_82V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S7_82V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ09876 (Selaginella moellendorffii), 3'ss of exon 10
cgggtacctgtgcgggagtgttcaggtgtgttagactagtcaaattcgcacaaatcattcgcgatatttgaagactcaccacaaggattcttttttg--cagACAAATGTGGGAACTGTGGATGCGCATGTTGCAGACTATCAGCAAATGATAGACAATCTTCAA
                                                     ||  | ||   |  ||  |  |     |  |   |||||  | |  |||||||||||||||||||||||||| ||||||||||| ||||| | |||||| ||||||||||| 
---------------------------------------------------gtatgttacgttgtgattacactccactaattacagttcttgatcgtccagACAAATGTGGGAACTGTGGATGCACATGTTGCAGATTATCAACGAATGATTGACAATCTTCAG

upper sequence: PP1S7_82V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ15186 (Selaginella moellendorffii), 3'ss of exon 10
cgggtacctgtgcgggagtgttcaggtgtgttagactagtcaaattcgcacaaatcattcgcgatatttgaagactcaccacaaggattcttttttg--cagACAAATGTGGGAACTGTGGATGCGCATGTTGCAGACTATCAGCAAATGATAGACAATCTTCAA
                                                     ||  | ||   |  ||  |  |     |  |   |||||  |||  |||||||||||||||||||||||||| ||||||||||| ||||| | |||||| ||||||||||| 
---------------------------------------------------gtatgttacgttgtgattacactccactaattacagttcttgattgtccagACAAATGTGGGAACTGTGGATGCACATGTTGCAGATTATCAACGAATGATTGACAATCTTCAG
















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: 17 (upstream exon), 19 (downstream exon)
Score: 1

CATGGTGGCAACAGTTTCTTGTGGCGCTGATCAATACCACCATACAACAAACACTCTCAAGTATGCGGACAGAGCCAAGGAGATTAAGACTCACATTCAGgtgttgactt ... ttttttgcagACAAATGTGGGAACTGTGGATGCGCATGTTGCAGACTATCAGCAAATGATAGACAATCTTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcacaaatcattcgcgatatttgaagactcaccacaaggattcttttttgcagACAAATGTGGGAACTGTGGATGCGCATGTTGCAGACTATCAGCAAATGATAGACAATCTTCAA
                           gactcac  putative branch site (score: 1)
                                          ttcttttttgc  putative PPT
                                         attctttttt  TA-rich tract