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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccacatctcaaattacacgtttcacatttcaagcctcctccccaatcttttttaagtatgagttgcctgtataatatcatcagtaggtttgcacatgaattcagataggagtgctggcagtctggctcagcactatatgtttttttgaattatttgctaaatgtgatataatgaccttattctttcagACAAGTGCATCTCTGAAGTTCACCGTTTTGAACCCAAAGGGGCGCATCTGGACAATGGTTGCTGGAGGTG

Basic information

species Oryza sativa
transcript LOC_Os11g47120.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 6
gtatccacatctcaaattacacgtttcacatttcaagcctcctccccaatcttttttaagtatgagttgcctgtataatatcatcagtaggtttgcacatgaattcagataggagtgctggcagtctggctcagcactatatgtttttttgaattatttgctaaatgtgatataatgaccttattctttcagACAAGTGCATCTCTGAAGTTCACCGTTTTGAACCCAAAGGGGCGCATCTGGACAATGGTTGCTGGAGGTG--------------------------
                 ||    | |||    |      |  ||    || |||| | ||   |  |  | ||||||| || ||||||               |||   ||| | | || |   |||||          | | || | ||||  | | |        | ||      ||||| || |||||||||||||| |||||||||||||| ||||||||||| || || ||||||||||| ||||| ||||| ||||                          
----------------gtattgatctcagggctatgtttttatcttttattttttctgag---gtctatcatgtataaaataatcagt---------------ttccattagaaatactag--atctgga--------gtgtattctgttgacgtgtgt--------taattcgccaaccttgttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA

upper sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatccacatctcaaattacacgtttcacatttcaagcctcctccccaatcttttttaagtatgagttgcctgtataatatcatcagtaggtttgcacatgaattcagataggagtgctggcagtctggctcagcactatatgtttttttgaattatttgctaaatgtgatataatgaccttattctttcagACAAGTGCATCTCTGAAGTTCACCGTTTTGAACCCAAAGGGGCGCATCTGGACAATGGTTGCTGGAGGTG--------------------------
                                                      |||||| ||     || | | ||| | || || |   ||||    | |     || ||   ||   | | | |  || | || |  |||| | | ||          |   ||||   |  | ||    || || ||||||||||| ||| |||||||||| |||||||| || || || ||||| ||||| ||||| ||||||||||                          
-----------------------------------------------------gtttaagcat--ccagcttttctaaaaacaccact---tttgtgactcagacaggaaagacttgaaagtaatgttactgaccatt-catgtctgtgtg----------tgtgtgtgtgtttgttac----ttattgcagACAAGTGCTTCTTTGAAGTTCACTGTTTTGAATCCTAAAGGCCGCATTTGGACGATGGTAGCTGGAGGTGGTGCTAGCGTCATATATGCTGATACA

upper sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 3'ss of exon 7
gtatccacatctcaaattacacgtttcacatttcaagcctcctccccaatcttttttaagtatgagttgcctgtataatatcatcagtaggtttgcacatgaattcagataggagtgctggcagtctggctcagcactatatgtttttttgaattatttgctaaatgtgatataatgaccttattct--ttcagACAAGTGCATCTCTGAAGTTCACCGTTTTGAACCCAAAGGGGCGCATCTGGACAATGGTTGCTGGAGGTG--------------------------
                                                                                         ||||| | ||  |  | ||||  |  || |  || ||      || | |    ||||   |   |     ||  || |||||  | | | ||||  ||  | ||||||||||||||| |||||||||| ||||||||||| || || ||||||||||| ||||| ||||||||||                          
------------------------------------------------------------------------------------tttctggttttctca--atctaagattagtctgtt--caatca----tagaaattggagtttacctatgta--cagcagaaagtgatccactaatcttacactggtgcagACAAGTGCATCTTTGAAGTTCACTGTTTTGAACCCCAAAGGACGCATCTGGACTATGGTAGCTGGAGGTGGTGCAAGTGTTATATATGCCGATACT

upper sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
gtatccacatctcaaattacacgtttcacatttcaagcctcctccccaatcttttttaagtatgagttgcctgtataatatcatcagtaggtttgcacatgaattcagataggagtgctggcagtctggctcagcactatatgtttttttgaattatttgctaaatgtgatataatgaccttattctttcagACAAGTGCATCTCTGAAGTTCACCGTTTTGAACCCAAAGGGGCGCATCTGGACAATGGTTGCTGGAGGTG--------------------------
                                                        |  |  ||| |    | | |||||    ||  |   |  || ||   | ||     || |     ||       ||  |   |  || |  |||      | | |    | | |  || ||    | |   | |||||  |||| |||||||| || ||  |  |||| || ||||| ||||| ||||||||||||||||||||||                          
-------------------------------------------------------gtgtgattgattcatttatctaata----caagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcattt-----ctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgtttttttgaattatttgctaaatgtgatataatgaccttattctttcagACAAGTGCATCTCTGAAGTTCACCGTTTTGAACCCAAAGGGGCGCATCTGGACAATGGTTGCTGGAGGTG
                     tgctaaa  putative branch site (score: 2)
                                         ccttattctttc  putative PPT
      tttttttgaattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccacatctcaaattacacgtttcacatttcaagcctcctccccaatcttttttaagtatgagttgcctgtataatatcatcagtaggtttgcacatgaattcagataggagtgctggcagtctggctcagcactatatgtttttttgaattatttgctaaatgtgatataatgaccttattctttcagACAAGTGCATCTCTGAAGTTCACCGTTTTGAACCCAAAGGGGCGCATCTGGACAATGGTTGCTGGAGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG