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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgagatggtctatcatgcaattttttgttattagtcttgtattcttcttctttttagttttaatttatatagttattagaatcttgtattgtcttccagGCTTTTCTCTTGTGGAACAAGTAAAGATGGTGAATCTCACCTAGTTGAATGGAATGAGAGCGAAGGAGCTATTAAACGGACATATTTAGGTTTTAGGAAA

Basic information

species Vitis vinifera
transcript Vv16s0039g02410.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02410.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os08g06480.1 (Oryza sativa), 3'ss of exon 14
atgagatggtctatcatgcaattttttgttattagtc-ttgtattcttcttctttttagttttaatttatat-agttattagaatcttgtattgtcttccagGCTTTTCTCTTGTGGAACAAGTAAAGATGGTGAATCTCACCTAGTTGAATGGAATGAGAGCGAAGGAGCTATTAAACGGACATATTTAGGTTTTAGGAAA
   | |   | |||| |    | | | |||   | |  || | |   ||   ||   | |||  || | |   |||| || || | |    ||  | | |||||| ||||| ||||| || || ||||||||||| || ||| | ||||| ||||||||||  || |||||||||||  |||||||    ||||| ||||| 
--tatacattttatcgtagcttctctagttgcaatttgttttgtcactccatttcacactttgtatctgtgcgagttgtttgattgtaaattttccctgcagGCTCTTCTCATGTGGTACTAGCAAAGATGGTGATTCACACTTGGTTGAGTGGAATGAGACTGAGGGAGCTATTAAGAGGACATACAATGGTTTCAGGAAG

upper sequence: Vv16s0039g02410.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 14
atgagatggtctatcatgcaattttttgttattagtcttgtattcttcttctttttagttttaatttatatagttattagaatcttgtattgtcttcc-------agGCTTTTCTCTTGTGGAACAAGTAAAGATGGTGAATCTCACCTAGTTGAATGGAATGAGAGCGAAGGAGCTATTAAACGGACATATTTAGGTTTTAGGAAA
    |||| | ||   | ||   |||  |  |   |||     | |||||   | |||   ||   |  ||| | |||    ||   | || ||||         ||||| |||||||| ||||||||||||||||| || ||| | || || |||||||||||||| || || || || || |||||||| | ||||||  |||| 
-aatgatgatttactgt-cagaatttgatcctccatct-----ttttcttacatgtagaggtatcgtgaatattgatttatctccccttttctctttttgatgttagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG

upper sequence: Vv16s0039g02410.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 14
atgagatggtctatcatgcaattttttgttattag----tcttgtattcttcttctttttagttttaatttatatagttattagaatcttgtat-tgtcttccagGCTTTTCTCTTGTGGAACAAGTAAAGATGGTGAATCTCACCTAGTTGAATGGAATGAGAGCGAAGGAGCTATTAAACGGACATATTTAGGTTTTAGGAAA
       | | |   ||  | ||   ||   ||||    |  ||| | | |||| | |||      |   | | |  |||| |   | || | | ||    |||| || || ||||||||||| || |||||||| |||||| | || || |||||||||||||||||||| || ||||| |||||||| | ||||||  | || 
-----tcgctttcgaattaagttgagtgaatttaggacgtgatgtgtccatcttgtatttgcgacaatgatttttgattatgaattttttctttgtggacgccagACTCTTTTCTTGTGGAACTAGCAAAGATGGAGAATCTTATCTGGTGGAATGGAATGAGAGCGAAGGCGCAATTAAGCGGACATACTCAGGTTTCCGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttctttttagttttaatttatatagttattagaatcttgtattgtcttccagGCTTTTCTCTTGTGGAACAAGTAAAGATGGTGAATCTCACCTAGTTGAATGGAATGAGAGCGAAGGAGCTATTAAACGGACATATTTAGGTTTTAGGAAA
             ttttaat  putative branch site (score: 3)
                                            ttgtcttcc  putative PPT
      tttttagttttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgagatggtctatcatgcaattttttgttattagtcttgtattcttcttctttttagttttaatttatatagttattagaatcttgtattgtcttccagGCTTTTCTCTTGTGGAACAAGTAAAGATGGTGAATCTCACCTAGTTGAATGGAATGAGAGCGAAGGAGCTATTAAACGGACATATTTAGGTTTTAGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - -tcatgca