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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acctcgaaccgcatgagggatcgggtgtgttgtgtccacagtgggttttttcgcattagtcttgtttgttttctaacgttatttctactttattttgcagAAAGCTCATGTTCAGCAATTTATGGCCACCGAAGATGCCTTGAATCAGGTGGCGCAAGCCAAAAGAATGACCAATGAACTCATTAGGCGGGTACGTGGTA

Basic information

species Physcomitrella patens
transcript PP1S189_50V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S189_50V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 3
acctcgaaccgcatgagggatcgggtgtgttgtgtccacagtgggttttttcg-cattagtcttgtttgttttctaacgttatttctactttattttgcagAAAGCTCATGTTCAGCAATTTATGGCCACCGAAGATGCCTTGAATCAGGTGGCGCAAGCCAAAAGAATGACCAATGAACTCATTAGGCGGGTACGTGGTA
                  |    | |   |  | |  || |    |||| | | ||| ||    |||  |   ||   | | | |||   ||      ||||||||||||||||| |||||| |||| || ||||||||  | ||  |||  ||  |||| |     |||    |  |||| || |  ||  | | |||  
------------------gtcttgattcatcat-taaactgcatattttgttgtcataagaggagttattgaactggtgctgtatctctgtt----cacagAAAGCTCATGTTCAACAATTTTTGGCTACTGAAGATGCACTAAACAAGGCTGCAGAAGCAAGGGATATGTGTGAAAAACTTATGAAACGTTTGCATGGAG

upper sequence: PP1S189_50V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA18G50960.1 (Glycine max), 3'ss of exon 3
acctcgaaccgcatgagggatcgggtgtgttgtgtccacagtgggttttttcg-cattagtcttgtttgttttctaacgttatttctactttattttgcagAAAGCTCATGTTCAGCAATTTATGGCCACCGAAGATGCCTTGAATCAGGTGGCGCAAGCCAAAAGAATGACCAATGAACTCATTAGGCGGGTACGTGGTA
                 ||      |   |  | |  || |    |||| | | ||| ||    |||  |   ||   |   | |||   ||      ||||||||||||||||| |||||| |||| || ||||||||  | ||  | |  ||  |||| |     |||    |  |||| || |  ||  | | |||  
-----------------ggtctttattcatcct-taaactgcatattttgttgtcataagaggagttattgaactggtgccgtatctctgtt----cacaGAAAGCTCATGTTCAACAATTTTTGGCTACTGAAGATGCACTAAACAAAGCTGCAGAAGCAAGGGACATGTGTGAAAAACTTATGAAACGTTTGCATGGA-

upper sequence: PP1S189_50V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ26051 (Selaginella moellendorffii), 3'ss of exon 4
acctcgaaccgcatgagggatcgggtgtgttgtgtccacagtgggttttttcgcattagtcttgtttgttttc-taacgttatttctactttattttgcagAAAGCTCATGTTCAGCAATTTATGGCCACCGAAGATGCCTTGAATCAGGTGGCGCAAGCCAAAAGAATGACCAATGAACTCATTAGGCGGGTACGTGGTA
                                     | || ||  |     |  || |||||  || |  || | |   | | |    |||   ||||||||||||||||||||||| |||||||| || ||||| || |||||  | |  ||| | ||||||      | | |  |  | || | |  | |   |||| 
-----------------------------------gtatagcggaatacaaggtttttgtctttcttctagtcatgaaagtgtct----tttgcgttgcagAAAGCTCATGTTCAGCAGTTTATGGCAACGGAAGAAGCATTGAACGAAGCTGCGGAGGCCAAAGCTGCAAGCGACAAGTTAATCAAGTCGCTCACTGGTG

upper sequence: PP1S189_50V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ26048 (Selaginella moellendorffii), 3'ss of exon 14
acctcgaaccgcatgagggatcgggtgtgttgtgtccacagtgggttttttcgcattagtcttgtttgttttctaacgtt--atttctactttattttgcagAAAGCTCATGTTCAGCAATTTATGGCCACCGAAGATGCCTTGAATCAGGTGGCGCAAGCCAAAAGAATGACCAATGAACTCATTAGGCGGGTACGTGGTA
                                                           | |||| | | |||||    |  |  | |  |||   ||||||||||||||||||||||| |||||||| || ||||| || |||||  | |  ||  | ||||||      | | |  |  | || | |  | |  ||||| 
---------------------------------------------------------gtttttgtctttcttctagtcatgaaagtgtcttttgcgttgcagAAAGCTCATGTTCAGCAGTTTATGGCAACGGAAGAAGCTTTGAACGAAGCTGCAGAGGCCAAAGCTGCAAGCGACAAGTTAATCAAGTCGCTCAGTGGTG

upper sequence: PP1S189_50V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ14453 (Selaginella moellendorffii), 3'ss of exon 4
acctcgaaccgcatgagggatcgggtgtgttgtgtccacagtgggttttttcgcattagtcttgtttgttttctaacgtt--atttctactttattttgcagAAAGCTCATGTTCAGCAATTTATGGCCACCGAAGATGCCTTGAATCAGGTGGCGCAAGCCAAAAGAATGACCAATGAACTCATTAGGCGGGTACGTGGTA
                                           |  |  | |   ||  | || | | | |||||    |  |  | |  |||   ||||||||||||||||||||||| |||||||| || ||||| ||  ||||  | |  ||| | ||||||      | | |  |  | || | |  | |  ||||| 
-------------------------------------------gtataatgcaagttgtttttatctttcttctagtcatgaaagtgtcttttgcgttgcagAAAGCTCATGTTCAGCAGTTTATGGCAACGGAAGAAGCTCTGAACGAAGCTGCGGAGGCCAAAGCTGCAAGCGACAAGTTAATCAAGTCGCTCAGTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcgcattagtcttgtttgttttctaacgttatttctactttattttgcagAAAGCTCATGTTCAGCAATTTATGGCCACCGAAGATGCCTTGAATCAGGTGGCGCAAGCCAAAAGAATGACCAATGAACTCATTAGGCGGGTACGTGGTA
                         ttctaac  putative branch site (score: 1)
                                    tttctactttatttt  putative PPT
                                 ttatttctactttatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acctcgaaccgcatgagggatcgggtgtgttgtgtccacagtgggttttttcgcattagtcttgtttgttttctaacgttatttctactttattttgcagAAAGCTCATGTTCAGCAATTTATGGCCACCGAAGATGCCTTGAATCAGGTGGCGCAAGCCAAAAGAATGACCAATGAACTCATTAGGCGGGTACGTGGTA

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