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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatttgattttttcctacctgagaaatagattttgttcttccacttccatgcacagccgaagtctaaattggcggacacttatcattgatccttactataatttttgttgtacccatccggacttttgcagTACGGACAATTCGATAAAAAATCACTGGAACAGCACAATGAAGAAGAAAGTGGATCCCTTGACGGCAAATGATCCAATCTCTAAAGCGCTGGCTGTCTAT

Basic information

species Physcomitrella patens
transcript PP1S120_159V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S120_159V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os01g12860.1 (Oryza sativa), 3'ss of exon 6
gtaattatttgattttttcctacctgagaaatagattttgttcttccacttccatgcacagccgaagtctaaattggcggacacttatcattgatccttactataatttttgttgtacccatccggacttttgcagTACGGACAATTCGATAAAAAATCACTGGAACAGCACAATGAAGAAGAAAGTGGATCCCTTGACGGCAAATGATCCAATCTCTAAAGCGCTGGCTGTCTAT
                 | ||   || | |||  ||| |  |  |  | ||   |  | |  |    | || | |   | |      |||||||   ||  || |||| | |||   || ||| ||||           ||||||||| || |||||||||||||||||  || | |||||||||||  || | |  | | ||   | |  | |  |  |||    |  | ||  |
----------------gtact-tttgtgcaattaattcttcttgttaatttttttaaaaaaacctcttttagactattgaa-----gtcattgaatttt--taaaattct-gtttcccctatcagGAC-----------GGACAATTCAATTAAAAATCACTGGAACAGTTCAGTAAAGAAGAAAGTCAATTCATACATGTCATCAGGTTTACTTACCCAAGTTTCGTGTCTCCCT

upper sequence: PP1S120_159V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT4G32730.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaattatttgattttt-----tccta-cctgagaa-atagattt----tgttcttccacttccatgc---acagccgaagtc-taaattg-----gcggacacttatcattgatc---cttactataat--ttttgttgtacccatccggacttttgcagTACGGACAATTCGATAAAAAATCACTGGAACAGCACAATGAAGAAGAAAGTGGATCCCTTGACGGCAAATGATCCAATCT-CTAAAGCGCTGGCTGTCTAT
|||| ||| |  |||       |||||   | | || |||| | |    ||| | |  | ||    ||   | |   ||| |  ||  ||      || |  | || |  |  |||   | | || |  |  |||  || |            |  || ||  | || ||||||||||||||||| ||||||||| || | ||||||||  ||||| |||     |||   | ||   |     |  |     |||  | | 
gtaaatatgtcttttccatgggtcctagtataacaacataggtgtaacatgtccgtaaaattggtggcctcataaatgaaataataggtttttgatgctggtagttgtggtctatcgttcctgctttggtgatttgcttattttttcttacgttcctgtagGTCAGATAATTCGATAAAAAATCATTGGAACAGCTCAGTTAAGAAGAAGTTGGATTCCTACTATGCATCAGGTCTTTTAGATCAGTGTCAAAGCTCGCCA-

upper sequence: PP1S120_159V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ27664 (Selaginella moellendorffii), 3'ss of exon 5
gtaattatttgattttttcctacctgagaaatagattttgttcttccacttccatgcacagccgaagtctaaattggcggacacttatcattgatccttactataatttttgttgtaccc-atccggacttttgcagTACGGACAATTCGATAAAAAATCACTGGAACAGCACAATGAAGAAGAAAGTGGATCCCTTGACGGCAAATGATCCAATCTCTAAAGCGCTGGCTGTCTAT
                                                                                       |   || ||||   | |  |   |  |   ||  |      | ||| ||| ||||||||||| || || |||||||||||||| || ||||||||||| || |||||       |||||||| || || || ||||| || || | ||||
--------------------------------------------------------------------------------------gtaggtgctcctgcttctgttgaataatcggcctgacttccgcatttacagGACGGACAATTCCATCAAGAATCACTGGAACAGTACCATGAAGAAGAAGGTTGATCCAGCACTTGCAAATGACCCGATTTCGAAAGCCCTCGCAGACTAT

upper sequence: PP1S120_159V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ37285 (Selaginella moellendorffii), 3'ss of exon 2
gtaattatttgattttttcctacctgagaaatagattttgttcttccacttccatgcacagccgaagtctaaattggcggacacttatcattgatccttactataatttttgttgtacccatccggacttttgcagTACGGACAATTCGATAAAAAATCACTGGAACAGCACAATGAAGAAGAAAGTGGATCCCTTGACGGCAAATGATCCAATCTCTAAAGCGCTGGCTGTCTAT
                                                                                  |  ||    || | ||   |  |||  | |   |  |  ||||  | ||| ||| ||||||||||| || || |||||||||||||| || ||||||||||| ||                                                 
--------------------------------------------------------------------------------gtaggtactcctgcttctg--ttgaataatcggcctgact-tccg--catttacagGACGGACAATTCCATCAAGAATCACTGGAACAGTACCATGAAGAAGAAGGTT------------------------------------------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttatcattgatccttactataatttttgttgtacccatccggacttttgcagTACGGACAATTCGATAAAAAATCACTGGAACAGCACAATGAAGAAGAAAGTGGATCCCTTGACGGCAAATGATCCAATCTCTAAAGCGCTGGCTGTCTAT
             tccttac  putative branch site (score: 2)
                                              cttttgc  putative PPT
                ttactataatttttgt  TA-rich tract