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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaagattttagattgatattaatatattatgcagagaaacaaacagtgttttgtccttcaatttttatatttatttaacattatccaattttttcaagGTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATT

Basic information

species Vitis vinifera
transcript Vv11s0052g00320.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os02g08018.1 (Oryza sativa), 3'ss of exon 6
taaaagattttagattgatattaatatattatgcagagaaacaaacagtgttttgtccttcaatttttatatttatttaacattatccaattttttcaagGTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATT
   ||||||    ||  | ||  ||  ||| ||    ||   |     | |  |||   | | || | | |||    | | | ||   |    ||| | |||||| ||||||||  ||||| ||  |||||| |||||||| ||||||||||| || |||||||| || |||||||| 
-gtaagatt----atgtaaatccatgcattctgatttgatttatgttctatgctgtttgt-atttctgagattataatgaaactaaatacacctttta-gGTCCCGGCTGATGGTGTTTTGGTTAGTGGTCATTCTCTTGCCATTGATGAATCCAGTATGACTGGGGAAAGCAAGATC

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G391042_T02 (Zea mays), 3'ss of exon 9
taaaagattttagattgatattaatatattatgca-gagaaacaaacagtgttttgtccttcaatttttatatttatttaacattatccaattttttca--agGTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATT
              | || |  ||   |||  ||| |||   |||     | ||  |   || ||||| |  |    |  | |   |  ||||| ||    |||||||  | ||||| ||  | ||   ||||||||| ||| | || ||||||||||||||||||||||| || || |||
-------------gtagaga--aagccattgagcatgagcctcaattttcgattcatgtgtctattttcaattcctatggataccttataatttctttgccagGTCCCCACAGATGGTATCCTTATCAGTGGTCACTCCCTTTCCATAGATGAATCAAGCATGACTGGAGAAAGTAAAATT

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 11
taaaagattttagattgatattaatatattatg-cagagaaacaaacagtgttttgtccttcaatttttatatttatttaacattatccaattttttcaagGTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATT
                        ||| |  || ||      || |   ||  |  |  || ||||||| | ||  ||     ||| |  || ||||| ||||||||||||||||| |||||||  ||||||||||||||||||||||||||||||| |||||||| ||||||||||||
-----------------------gtatgtcttgtcatttttgcatatcatgcctaatggttgaattttt-tgttatttagttcttaactgatcttttctagGTCCCTGCTGATGGAGTTTTGATCACTGGTCACTCTCTTGCAATTGATGAATCAAGTATGACTGGGGAGAGCAAGATT

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 8
taaaagattttagattgatattaatatattatgcagagaaacaaacagtgttttgtccttcaatttttatatttatttaaca-ttatccaattttttcaagGTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATT
                       || | |||| ||      || |   ||  |  |  ||  ||||||    |||||||    ||| |  || ||||| ||||||||||||||||| |||||||  | ||||||||||||||||||||||||||||| |||||||| ||||||||||||
---------------------gtatgtcttat-catttttgcatatcatgcctaatggttgcattttttg--ttatttagtgcttaactgatcttttctagGTCCCTGCTGATGGAGTTTTGATCACCGGTCACTCTCTTGCAATTGATGAATCAAGTATGACTGGGGAGAGCAAGATT

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 8
taaaagattttagattgatattaatatattatgcagagaaacaaacagtgttttgtccttcaatttttatat-ttatttaacattatccaattttttcaagGTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATT
              ||||| ||  | ||||||           | ||   ||||   || || ||| | | | ||||| |    | | | | | |||| |||||||||||||||||||| ||||  |||| |||||||||||||||||||||||||| |||||||| |||||||| |||
----------gtacttgatctttttctattattgttttttcttatcatactttttgactgcattttctctttgttattaagttcttttctactctttctagGTCCCTGCTGATGGAATTCTGATCACTGGCCACTCTCTTGCAATTGATGAATCAAGTATGACTGGGGAGAGCAAAATT

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 8
-taaaagattttagattgatattaatatattatgcagagaaacaaacagtgttttgtccttcaatttttatatttatttaacattatccaattttttcaagGTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATT
 |||  ||||||   ||  ||||| | | || |        ||      ||  | |   ||| |||| |     |||| |    | | | | | |||| ||||||||||||||||| || ||||  |||| |||||||||||||||||||||||||| |||||||| |||||||| |||
gtaattgattttttttttctattattgttttttcttatcttact-----tgactggattttctatttgt-----tattaagttcttttctactctttctagGTCCCTGCTGATGGAGTTCTGATCACTGGCCACTCTCTTGCAATTGATGAATCAAGTATGACTGGGGAGAGCAAAATT

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 10
taaaagattttagattgatattaatatattatgcagagaaacaaacagtgttttgtccttcaatttttatatttatttaacattatccaattttttcaagGTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATT
                |  | |  | |||| | |    ||          |||||||| |  |||    | | || |  |  || |  | || | || |||| |||||||||||| |  |||| ||||| |||||||| ||  |||||||||| |||||||||||||||||||| |||
----------------gtgagtggtttattctccttttaattttgt----ttttgtccat--attaccttgtctaatcgaagtt-taaatttatatctagGTTCCTGCTGATGGAGTACTGATATCTGGCCACTCTCTCGCCCTTGATGAATCTAGCATGACTGGAGAGAGCAAAATT

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 10
taaaagattttagattgatattaatatattatgcagagaaacaaacagtgttttgtccttcaattt--ttata-tttatttaacattatccaattttttca--agGTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATT
    |  ||| |   |  | | |||  | |||           | |  | ||  |   |||| | |   |||| ||||| |   ||   |||||  ||||   |||| ||||| |||||| ||||  || |||| || || |||||| ||||||| || |||||||||||||||||||| |||
--gcaagtttcatgattttgtcaatgcagtatttc------ttagctcttttccgaatttcagtatagctataatttatgtttgatctgccaataatttccatagGTACCTGCGGATGGAGTTTTAGTTGCTGGACATTCCCTTGCAGTTGATGAGTCCAGCATGACTGGAGAGAGCAAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgttttgtccttcaatttttatatttatttaacattatccaattttttcaagGTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATT
                             atttaac  putative branch site (score: 3)
                                             ttttttc  putative PPT
             ttcaatttttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaagattttagattgatattaatatattatgcagagaaacaaacagtgttttgtccttcaatttttatatttatttaacattatccaattttttcaagGTCCCTGCTGATGGAATTTTGATTTCTGGTCACTCTCTTGCAATTGATGAATCAAGCATGACTGGAGAGAGCAAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
-aaaagat
- - - - - - - - - - - - - - -tatgcag
- - - - - - - - - - - - - - - - - - - aaacaaa