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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcattactaaatttgcaaaatatttgttaaattatctgcttttatgctggtatgcttaaattttataataggagttgtgaatttatttatttatatagtaattgttattgtttggccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTGTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC

Basic information

species Vitis vinifera
transcript Vv05s0020g00570.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00570.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G07200.1 (Glycine max), 3'ss of exon 1
gtttgtcattactaaatttgcaaaatatttgttaaattatctgcttttatgctggtatgcttaaattttataataggagttgtgaatttatttatttatatagtaattgttattgtttggccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTGTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC
                                    ||   | ||||  || || | || |||| |||  |  |    ||| | | ||    |    |  |  | ||| ||  ||  |  |  ||  |||| || ||||| || || ||||||||||||||  ||||| | ||||| ||||||||||| ||||| ||||||||| | | |||| |  |||| || ||| 
-----------------------------------gttggtttctttgttgatgttgtg-ttaattttggtttt----gttttcatttctactgcgaaatt--tgattattgatggataact-ttacagATAGACAAGGCGTACCCTCGTGATTTCATGCAGAGAGGGCGCGTGAGGGTGTTGCTGAAGAAGGAGGATGGAACTCTCTTTAATTCAACCATCTCATCCA
















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|71890504|gb|DT039559.1|DT039559
EST:     CCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|77580101|gb|DV218940.1|DV218940
EST:     CCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|110364564|gb|EC927913.1|EC927913
EST:     CCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|71868537|gb|DT017592.1|DT017592
EST:     CCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|71867217|gb|DT016272.1|DT016272
EST:     CCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|77586586|gb|DV222418.1|DV222418
EST:     CCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGAT
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGAT
EST: gi|22008948|gb|BQ793982.1|BQ793982
EST:     CCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|110375143|gb|EC940104.1|EC940104
EST:     CCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|110416251|gb|EC982219.1|EC982219
EST:     CCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|30128384|gb|CB913723.1|CB913723
EST:     TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|110407038|gb|EC972629.1|EC972629
EST:     CCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|71866966|gb|DT016021.1|DT016021
EST:     CCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|83275344|gb|DV939352.1|DV939352
EST:     CGAAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: CG-AGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|83275320|gb|DV938471.1|DV938471
EST:     CCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|110378561|gb|EC943698.1|EC943698
EST:     CCGAGATTGGTGACTGTTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
EST: gi|110385463|gb|EC949995.1|EC949995
EST:     CCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAG                         ATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG
genomic: TCGAGATTGGTGACTGCTGCAGCCATCTCAAACTCCCATTTGCAATTGAGgtttgtcatt ... gccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggagttgtgaatttatttatttatatagtaattgttattgtttggccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTGTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC
     ttgtgaatttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtcattactaaatttgcaaaatatttgttaaattatctgcttttatgctggtatgcttaaattttataataggagttgtgaatttatttatttatatagtaattgttattgtttggccattgaagATTGATAAGGCATATCCACGTGATTTCATGCAACGAGGGAGAGTGAGAGTGTTGCTGAAAAAGGAAGATGGAACTTTATATAATCCTGCCATTTCTTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA