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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtatatttctcttcgtgatcaaccgattatctttcagcttgaattttcgaagtcagttctaatatctgtgtttctcaaatttcacttttgagatgcagTTCCGGCAATTTGCTAATAAGATTGGAAATCTTGAGCGTCCATTTCTTAAAGAATTTTTTCAGCGATGGGTTGCATCTTATGGTTGTCCCGTGCTAAG

Basic information

species Arabidopsis thaliana
transcript AT1G73960.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G73960.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA17G13080.1 (Glycine max), 3'ss of exon 11
-ttgtatatttctcttcgt--gatcaaccgattatctttcagcttgaattttcgaagtcagttctaatatctgtgtttctcaaatttcacttttgagatgcagTTCCGGCAATTTGCTAATAAGATTGGAAATCTTGAGCGTCCATTTCTTAAAGAATTTTTTCAGCGATGGGTTGCATCTTATGGTTGTCCCGTGCTAAG
 | || || |  ||   ||   || ||| ||      ||   |||||    |     |      ||  || ||  | |    | |||   |||  | |||||||| || || |||||||| ||| |||| |||||||| || |||||||||||||| || ||||  || |||||||  |||| ||| ||||| ||  ||||
gtagtttaatcttcaatgttgtattaactgaagcatcttattcttgacgggttttgcttgtcaatataatgtggatctgatcatttt---tttcaatatgcagTTTCGACATTTTGCTAACAAGGTTGGGAATCTTGAACGCCCATTTCTTAAAGATTTCTTTCCTCGGTGGGTTGGTTCTTGTGGATGTCCTGTTTTAAG

upper sequence: AT1G73960.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA05G07920.1 (Glycine max), 3'ss of exon 11
ttgtatatttctcttcgtgatcaaccgat-tatctttcagcttgaattttcgaagtcagttctaata-tctgtgtttc-tcaaatttcacttttgagatgcagTTCCGGCAATTTGCTAATAAGATTGGAAATCTTGAGCGTCCATTTCTTAAAGAATTTTTTCAGCGATGGGTTGCATCTTATGGTTGTCCCGTGCTAAG
   ||   |||  | |   || | | ||   ||||      |   |  ||     || ||    ||| | ||  |||  | |||    | |||  | |||||||| || || |||||||| ||| |||| |||||||| || |||||||||||||| || ||||  || |||||    |||| ||| ||||| ||  ||||
---taatcttcaatgctgtattagctgaagcatctaattcttgacaggttttggttctgtcaatatactgtggatttgataaaaaaaaaatttcaatatgcagTTTCGACATTTTGCTAACAAGGTTGGGAATCTTGAACGCCCATTTCTTAAAGACTTCTTTCCTCGGTGGGTCAGTTCTTGTGGATGTCCTGTTTTAAG

upper sequence: AT1G73960.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv17s0000g04200.t01 (Vitis vinifera), 3'ss of exon 11
---ttgtata-tttctcttcgtgatcaaccgattatctttcagcttgaattttcgaagtcagttctaatatctgtgtttctcaaatttcacttttgagatgcagTTCCGGCAATTTGCTAATAAGATTGGAAATCTTGAGCGTCCATTTCTTAAAGAATTTTTTCAGCGATGGGTTGCATCTTATGGTTGTCCCGTGCTAAG
   | || || |||   | | | || |    |||||  |       |||| |      | | ||    ||  | | |  || || |    || |  |  |||||||||| || ||||| |||||| |||||||||||||||| ||||||||||||||||||||||  || ||||| | ||||| ||| ||||| || |||||
ttttggtgtaatttgaatacatcatgattttattattgtgttagaagaatatgt----ttattttatttacttatttaccttaattaatcctataaatgtgcagTTCCGACATTTTGCCAATAAGGTTGGAAATCTTGAGCGCCCATTTCTTAAAGAATTTTTTCCTCGCTGGGTAGGATCTTGTGGGTGTCCTGTACTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcgaagtcagttctaatatctgtgtttctcaaatttcacttttgagatgcagTTCCGGCAATTTGCTAATAAGATTGGAAATCTTGAGCGTCCATTTCTTAAAGAATTTTTTCAGCGATGGGTTGCATCTTATGGTTGTCCCGTGCTAAG
             ttctaat  putative branch site (score: 2)
                                    tttcactttt  putative PPT
             ttctaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtatatttctcttcgtgatcaaccgattatctttcagcttgaattttcgaagtcagttctaatatctgtgtttctcaaatttcacttttgagatgcagTTCCGGCAATTTGCTAATAAGATTGGAAATCTTGAGCGTCCATTTCTTAAAGAATTTTTTCAGCGATGGGTTGCATCTTATGGTTGTCCCGTGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - -tctcttc
- - - - - - - - - - -caaccga
- - - - - - - - - - - - - - - - ctttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctcaaa