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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCGTGTATCATAAGgttagacccagactctacatacactttttccagattcactgattgtacaactgtggtgcagattttgtttttgcaacatttctccaatttaccagtctcc...

Basic information

species Physcomitrella patens
transcript PP1S154_52V6.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S154_52V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 12
CAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCGTGTATCATAAGgttagacccagact-ctacatacactttttccagattcactgattgtacaactgtggtgcagattttgtttttgcaacatttctccaatt-taccagtctcc----------------------------------
|||||| ||||  ||||| ||||| ||||| ||  || ||||||| || ||||| |||||||||||||||||| | ||||||||||| || || || ||||| |   | ||  |  | | | | ||| || | |  ||  |||||   ||  | ||   ||   ||   | |         |||||  |   ||||    ||                                  
CAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaagcttattgcctgctcttgtttccgtatctgtgattcagca-ttatgtgccatgcttaactgtacaggttggtctcctgtggcaccatataccattctaacttcaagtaactctgtaccaattgcag

upper sequence: PP1S154_52V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 14
CAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCGTGTATCATAAGgttagacccagactcta-catacactttttccagatt--cactgattgt-acaac-tgtggtgcagattttgtttttgcaacatttctccaatttaccagtctcc----
|||||| |||| |||||| ||||| || || |||||| |||| ||||||||||||||||| || || |||||| ||||||||||||| || ||||| ||||| |   | ||  |||  | |   ||| |||| |     ||   ||||| || |  |||| | ||   ||  |   |   |  | |  | || ||  || |        
CAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAGgtaatcgcaagcttctggcttggtcttgttcccgtgcagcatgcattgttacgatgtgtgattcac-cttgatcagtaagatgtgttcctaacttcacactggttgcag

upper sequence: PP1S154_52V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GRMZM2G104920_T03 (Zea mays), 5'ss of exon 12
CAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCGTGTATCATAAGgttagacccagactctacat---acactttttccagattcactgattgt-acaac-tgtggtgcagattttgtttttgcaacatttctccaatttaccagtctcc----
||||||||||| |||||| ||||| ||||| || ||| |||| |||||||| |||||||| || || |||||  ||||||||||||| || ||||| ||||| |   | ||  |||        ||  ||  |  |   ||   ||||| |  |  ||||   || || |  |   |   |    |  | || |   || |        
CAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTGTTTATCACAAGgtaatggcaagcttctgtcctggtcatgttcccatgcagcatgcattgttatgatgtgtgactca-atataatcaatcagatgggttcctaactctacactgattgcag

upper sequence: PP1S154_52V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 12
CAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCGTGTATCATAAGgttag----acccagactctacata--cactttttccagattcactgattgtac-aactgtggtgcagattttgttttt--gcaacatttctccaatttaccagtctcc
|||||||||||| ||||||||||| || || ||  |  ||||||||| ||| |||||| | || || |||||| |||| || || ||||| || |||||||||||    |||    ||  | | |  || ||||     |||     ||| ||| ||   |      |||  |  || |  | |||  || | | ||||          
CAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCGTCTACCATAAGgttagtagtacctgatcttaaaacagccaattttcatgcattttactattatactaagaatccatttgatagtaattctaggaaacgcttttactatttt---------

upper sequence: PP1S154_52V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: Vv10s0523g00030.t01 (Vitis vinifera), 5'ss of exon 12
CAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCGTGTATCATAAGgttagacccagactctacatacactttttccagattcactgattgtacaactgtggtgcagattttgtttttgca-acatttctccaatttaccagtctcc
 ||||| ||  ||||||||||||||||||| ||  | || |||||||  || || |||||||| || |||||| |||| || || |||| |||||| ||||||| |   | |  || ||   |  |            ||  |   | |    |  |  |  |||||| ||  |   ||                      
TAGAGGGCATTCAAATGAGAAGAATTTTGTGGGTCTCACAGTAAACAGCGAATACATTGCCTGTGGCAGTGAAACAAACGAAGTGTTCGCGTATCACAAGgttaca---aaatacttcaagaagctagcattaggcatctagtcccaaat---taatttaatttttgtgttcacttgcag---------------------

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), 34 (downstream exon)
Score: 41

CAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCGTGTATCATAAGgttagaccca ... tctttggcagGCTATGTCGAGGCCAGCTTCGTGGCACAGATTTGGGTCCCACAACTCTGAAGATAACGGAGATGATAGTTCACACTTCATCAGTGCAGTTTGTTGGAAGA




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