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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCTgtaagtggtgcagaatctgcacattttcccatctgaattaggttttcctcagttcgccatgggattgcacctattgtttaggatcttaactctctctcaatttaaagacgtgatctgcgtttgtgttttcttgacttttgaaatctcctttgtttttcag

Basic information

species Physcomitrella patens
transcript PP1S114_2V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S114_2V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
TATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCTgtaagtggtgcagaatctgcacattttcccatctgaattaggttttcctcagttcgccatgggattgcacctattgtttaggatcttaactctctctcaatttaaagacgtgatctgcgtttgtgttttcttgacttttgaaatctcctttgtttttcag
||||||||| | ||  ||||||| |||||||| ||||||||||||||  | |||||||| || |||||||| |||||  | ||  | || ||||||  |   | |   | | | ||    | |||||  | |  ||     |||   |||  |        || |    | ||| |  | ||  |    | | ||  |   || ||          ||||| |  | || | |||| ||  ||| | |||
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagtt----acctgaacaaagcattgt---gttttacataag--------tagtaaaaaagatttccaatcaat----actcaagaa---gaact----------tttctggtttcttaatatcttctc-gttatgcag

upper sequence: PP1S114_2V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G006428_T02 (Zea mays), 5'ss of exon 10
TATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCTgtaagtggtgcagaatctgcacattttcccatctgaattaggttttcctcagttcgccatgggattg-cacctattgtttaggatcttaactctctctcaatttaaagacgtgatctgcgtttgtgttttcttgacttttgaaatctcctttgtttttcag
||||||||| | ||  ||||||| |||||||| ||||||||||||||  | ||||||||||| |||||||| |||||  | ||  | || ||||||  || |      ||| |  |  ||       |||  | | | |    | |   |  ||||| ||  |  ||  |     |  | |   || |    |  |                                                       
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattgaatg--tggcagaaatgacctgaaactttaaatctacatagcatggagttcagattgacaattgatgcatg----ccaagcatcctgttggctgga-------------------------------------------------------

upper sequence: PP1S114_2V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: EFJ15174 (Selaginella moellendorffii), 5'ss of exon 10
TATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCTgtaagtggtgcagaatctgcacattttcccatctgaattaggttttcctcagttcgc-catgggattgcacctattgtttaggatcttaactctctctcaatttaaagacgtgatctgcgtttgtgttttcttgacttttgaaatctcctttgtttttcag
|| |||||||| ||| |||| || |||||||||||||||||| | ||  | |||||||||||||| || || ||||| || |||||||| ||          || | | || ||||    ||||||  ||||  || || | ||||  ||||| |  |                                                                                             
TACGATGAAGCTGAGAGGAGGAGAGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgtt---------gagtttcca-atttgagtatctga--taggcctttctaacttcgttcatggtacag---------------------------------------------------------------------------------------------

upper sequence: PP1S114_2V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: EFJ08409 (Selaginella moellendorffii), 5'ss of exon 10
TATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCTgtaagtggtgcagaatctgcacattttcccatctgaattaggttttcctcagttcgc-catgggattgcacctattgtttaggatcttaactctctctcaatttaaagacgtgatctgcgtttgtgttttcttgacttttgaaatctcctttgtttttcag
|| |||||||| ||| |||| ||||||||||||||||||||| | ||  | |||||||||||||| || || ||||| || |||||||| ||          || | | || ||||    ||||||  ||||  || || | ||||| ||||| |  |                                                                                             
TACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgtt---------gagtttcca-atttgagtatctga--taggcctttctaacttcgctcatggtacag---------------------------------------------------------------------------------------------

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: 35 (upstream exon), 33 (downstream exon)
Score: 11

TATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCTgtaagtggtg ... tgtttttcagTCTAGGGCGAAGGCGCTTGCGGACCTTCAACAAATGCAGCCTGTGCAGATTGAAAAGTTAAGTGACAAACAATGTCAACCTGTGTCGCAGCTGAAGTTTG




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