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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaatgatttaatcatcacctttagaataaaaagtttccacacaatgtgtatagcaatttatttatttccttcccctggattcttgatctgtcttgcagTGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCTTTTGGCAATGGCAGAGGCAGAGCGGCATTTCTTGGAAGCTGAGTATGAT

Basic information

species Vitis vinifera
transcript Vv01s0026g02470.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G11960.1 (Glycine max), 3'ss of exon 4
caaaatgatttaatcatcacctttagaataaaaagtttccacacaatgtgtatagcaatttattt----atttccttcccctg-gattcttgatctgtcttgcagTGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCTTTTGGCAATGGCAGAGGCAGAGCGGCATTTCTTGGAAGCTGAGTATGAT
    | | |  |||  ||   |||| | |   |  |    |     | | ||||   || || ||    | ||   |||     || |  ||| |  |||||||| || ||||||||||| |||||||| || ||||| |||||||||||||| || |||||||| ||||||||||| || || |||||||| ||||| ||||||
--gtaagctaaaattttctattttaaagttgtatttgattatgttctatatatacttatataatttgaaacttgtctccttaacgagttatgacc-atcttgcagAGGTGGCTGGACAATATCTGGCACACCCTTGGACTTGCGTGATCCTCGACTCTTGGCAATTGCAGAGGCAGAACGTCAGTTCTTGGATGCTGAATATGAT

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G04870.1 (Glycine max), 3'ss of exon 3
---------------------------------------caaaatgattt-aatcatcacctttagaataaaaagtttccacacaatgtgtatagcaatttatttatttccttcccctggattcttgatctgtcttgcagTGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCTTTTGGCAATGGCAGAGGCAGAGCGGCATTTCTTGGAAGCTGAGTATGAT
                                        ||| |  |||  |  |  | |  |  | | |||   ||  ||| | | ||| |   | | |  || ||||  ||    |   |  ||||   | |||||||||||||||||||||||||||||| || ||||| ||||||||||| || || || ||||| |||||||| || || || |||||||||||||| || |||
gtaagctggaagcttcttttttaaaagtcttcattccagtaaattagttttgaatacaagcaatctatttaaactcttggacatatt-tgtttcaaagtcttgttgtttcactcattag---ttatgattgtttttgcagTGGAGGCTGGACAATCTCTGGCACGCCATTGGACTTGCGTGATCCCCGACTCTTAGCAATTGCAGAGGCTGAACGTCAATTCTTGGAAGCTGAATACGAT

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G05800.1 (Glycine max), 3'ss of exon 4
caaaatgatttaatcatcacctttagaataaaaagtttccacacaatgtgtatagcaatttatttatttccttcccctg--gattcttgatctgtcttgcagTGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCTTTTGGCAATGGCAGAGGCAGAGCGGCATTTCTTGGAAGCTGAGTATGAT
     | |  | |     |  || |   |  |   |||    |   | | ||  |   | | |  |  |  |  || |   || |  ||| |  |||||||| || ||||||||||| |||||||| || || || |||||||||||||| || |||||||| ||||| ||||| || || |||||||| ||||| ||||||
----gtaagctgaattctattttaaagttgta---tttgtttatgttctttagtgttttctttgaaacttatctccttaacgagttatgacc-atcttgcagAGGTGGCTGGACAATATCTGGCACACCCTTAGACTTGCGTGATCCTCGACTCTTGGCAATTGCAGAAGCAGAACGTCAGTTCTTGGATGCTGAATATGAT

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G35750.2 (Glycine max), 3'ss of exon 3
------caaaa-----tgatttaatcatcacc--tttagaataaaaagtttccacacaatgtgtatagcaatttatttatttccttcccctggattcttgatctgtcttgcagTGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCTTTTGGCAATGGCAGAGGCAGAGCGGCATTTCTTGGAAGCTGAGTATGAT
      |||||     || |||||   ||     || || |||  |  | |  | ||||    | | |      | |  | |    | | |   || | |||   | | |||||||||||||||||||||||||||  || ||||| ||||||||| | || || || ||||| |||||||| || || || |||||||||||||| || |||
gtacgccaaaagttcctgttttaaaagtctttatttcagtatatcagttctgaatacaagccttgttgtttcaaagtcttgtttcactcattagttat-gattgttttggcagTGGAGGCTGGACAATCTCTGGCATGCCATTGGACTTGCGTGATACCCGGCTCTTAGCAATTGCAGAGGCTGAACGTCAATTCTTGGAAGCTGAATACGAT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|351030409|gb|FQ432347.1|FQ432347
EST:     ACTGCTCCTCCCCCACCACCTCATCCTGAAGATACTGCTATTGATATTGG                         TGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCT
genomic: ACTGCTCCTCCCCCACCACCTCATCCTGAAGATACTGCTATTGATATTGGgtatgttcaa ... tgtcttgcagTGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCT
EST: gi|110685836|gb|EE062903.1|EE062903
EST:     ACTGCTCCTCCCCCACCACCTCATCCTGAAGATACTGCTATTGATATTGG                         TGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCT
genomic: ACTGCTCCTCCCCCACCACCTCATCCTGAAGATACTGCTATTGATATTGGgtatgttcaa ... tgtcttgcagTGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCT
EST: gi|110689841|gb|EE066416.1|EE066416
EST:     ACTGCTCCTCCCCCACCACCTCATCCTGAAGATACTGCTATTGATATTGG                         TGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCT
genomic: ACTGCTCCTCCCCCACCACCTCATCCTGAAGATACTGCTATTGATATTGGgtatgttcaa ... tgtcttgcagTGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCT
EST: gi|110713173|gb|EE088860.1|EE088860
EST:     ACTGCTCCTCCCCCACCACCTCATCCTGAAGATACTGCTATTGATATTGG                         TGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCT
genomic: ACTGCTCCTCCCCCACCACCTCATCCTGAAGATACTGCTATTGATATTGGgtatgttcaa ... tgtcttgcagTGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCT
EST: gi|30298557|gb|CB975351.1|CB975351
EST:     ACTGCTCCTCCCCCACCACCTCATTCGGAAGATACTGCTATTGATATTGG                         TGGAGGCTGGACAATCTCTGGCACTCCTTTGGGTTTGCGTGATCCTCGCCT
genomic: ACTGCTCCTCCCCCACCACCTCATCCTGAAGATACTGCTATTGATATTGGgtatgttcaa ... tgtcttgcagTGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCT
EST: gi|110715491|gb|EE093604.1|EE093604
EST:     ACTGCTCCTCCCCCACCACCTCATTCTGAAGATACTGCTATTGATATTGG                         TGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCT
genomic: ACTGCTCCTCCCCCACCACCTCATCCTGAAGATACTGCTATTGATATTGGgtatgttcaa ... tgtcttgcagTGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgtatagcaatttatttatttccttcccctggattcttgatctgtcttgcagTGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCTTTTGGCAATGGCAGAGGCAGAGCGGCATTTCTTGGAAGCTGAGTATGAT
                                     tcttgat  putative branch site (score: 4)
                                           tctgtctt  CT-rich tract
     tatagcaatttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaatgatttaatcatcacctttagaataaaaagtttccacacaatgtgtatagcaatttatttatttccttcccctggattcttgatctgtcttgcagTGGAGGCTGGACAATCTCTGGCACTCCTTTGGATTTGCGTGATCCTCGCCTTTTGGCAATGGCAGAGGCAGAGCGGCATTTCTTGGAAGCTGAGTATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
-aaaatga
- - - - - - - catcacc
- - - - - - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - - - ccacaca