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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacagatcaagaaggttttctctttttgctgcatagcatatttcacacaataaatttgtgaagatttacttccattcatttcttttctgttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATTGTGAAGTTGCTTGATATTGTTAGAGATCAGCAATCAAAGACCCCAAGTC

Basic information

species Vitis vinifera
transcript Vv07s0129g00270.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0129g00270.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G17520.2 (Glycine max), 3'ss of exon 2
atacagatcaagaaggttttctctttttgc-tgcatagcatatttcacaca-ataaatttgtgaagatttacttccattcatttcttttctgttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATTGTGAAGTTGCTTGATATTGTTAGAGATCAGCAATCAAAGACCCCAAGTC
||| | ||  | |    | | | | | |   |  |||  |||| | | | | ||| || | |  | || ||  ||     ||   | |  |  | ||| |||||||||||||| || |||||| | ||||| |||||||| ||||| ||| |||| ||||||||||| ||||||||||| |||||||| |||||||||||||
atatatatatatatatatatatatatatatatatata-tatatat-atatatatatatatatataaatgtaactctgacaatgcttctgtttctgaatgcagATCAAGAGGGAAATCAAAATATTACAGAATCTTTGTGGAGGGCCTAATGTTGTAAAGTTGCTTGACATTGTTAGAGACCAGCAATCGAAGACCCCAAGTC

upper sequence: Vv07s0129g00270.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G22320.1 (Glycine max), 3'ss of exon 2
atacagatcaagaaggttttctctttttgctgcatagcatatttcaca---caataaatttgtgaagatttacttccattcatttcttttctgttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATTGTGAAGTTGCTTGATATTGTTAGAGATCAGCAATCAAAGACCCCAAGTC
      ||| ||  | || | |     |     |  |  | | |  ||   |  |   | | |  | || ||  |      ||   | |  |  | ||| |||||||||||||| || |||||| | ||||| |||||||| ||||| ||||||||  |||||||||| ||||||||||| || || || |||||||||||||
---gctatctagttgtttattttaaagtataataatgattgtcttccatccctctggttatatatatatgtaactttgacaatgattctggttctgaatgcagATCAAGAGGGAAATCAAAATATTACAGAATCTTTGTGGAGGGCCTAATATTGTACAGTTGCTTGACATTGTTAGAGACCAACAGTCGAAGACCCCAAGTC

upper sequence: Vv07s0129g00270.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 2
--------atacag--atcaagaaggttttctct---ttttgct----gcatagcatatttcacacaataaatttgtgaagatttacttcc--attcatttcttttctgttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATTGTGAAGTTGCTTGATATTGTTAGAGATCAGCAATCAAAGACCCCAAGTC
        ||||||          | |||| |||   || ||||        ||  | ||||   |  |  | |||    || ||| |  |  |   ||||   ||||  |  |  ||||| ||||| |||||||| || ||||||||||| || |||||||| |||||||| || ||||| || ||||||||||||||||| || ||||| || ||  
gtgagtagatacagccgcttgcttgtttttatctcaattgtgctcagaatgaagtgtgtttctggcccttcacttggtttgaattattctctaacatattttgcttctccttgacgcagATTAAGAGAGAGATTAAGATTCTGCAGAACCTCTGCGGTGGGCCTAATATTGTAAAATTGCTCGACATTGTTAGAGATCAGCAGTCTAAGACGCCCAGCT

upper sequence: Vv07s0129g00270.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------------------------------atacagatcaagaa-ggttttctctttttgctgcatagc-----atatttcacacaataaatttgtgaagatttacttcca--ttcatttcttttctgttaaat------acagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATTGTGAAGTTGCTTGATATTGTTAGAGATCAGCAATCAAAGACCCCAAGTC
                                                                                |   | ||||  ||  | |   || ||  || | | | |     ||| |||  ||  |        || |  |||  ||     |||| ||     | ||  ||      | ||||||| || ||||| || || ||||| ||||||||||| ||||| || ||||||||| | || || |||||  | ||||||||||| ||||| || || |
gtacctgactgctagtgatttttatggctggcgtcctagtttttagttgtgaagtttcaacaagtgacattttcttagttacttacatcagaaacagataattccttgggcagaacatctttaaataattcttacggtctgcaaaagatgtgttatctctgacctcatgtcaacaattttggatttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATTGTGAAGCTTCTGGACATTGTCCGTGATCAGCAATCGAAGACACCCAGCC

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|77589565|gb|DV224064.1|DV224064
EST:     AC-ATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAG                         ATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
genomic: ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAGgtgaggccct ... ttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
EST: gi|71883675|gb|DT032730.1|DT032730
EST:     AC-ATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAG                         ATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
genomic: ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAGgtgaggccct ... ttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
EST: gi|27586807|gb|CB009502.1|CB009502
EST:     ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAG                         ATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
genomic: ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAGgtgaggccct ... ttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
EST: gi|27586429|gb|CB009124.1|CB009124
EST:     ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAG                         ATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
genomic: ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAGgtgaggccct ... ttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
EST: gi|71883451|gb|DT032506.1|DT032506
EST:     AC-ATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAG                         ATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
genomic: ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAGgtgaggccct ... ttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
EST: gi|161717971|gb|FC069266.1|FC069266
EST:     ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAG                         ATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
genomic: ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAGgtgaggccct ... ttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
EST: gi|33402558|gb|CF208185.1|CF208185
EST:     ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAG                         ATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
genomic: ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAGgtgaggccct ... ttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
EST: gi|110717101|gb|EE092665.1|EE092665
EST:     ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAG                         ATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
genomic: ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAGgtgaggccct ... ttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
EST: gi|110703175|gb|EE079801.1|EE079801
EST:     ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAG                         ATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT
genomic: ACAATGAGAAGTGTATTATTAAGATACTCAAACCCGTGAAAAAGAAAAAGgtgaggccct ... ttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacaataaatttgtgaagatttacttccattcatttcttttctgttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATTGTGAAGTTGCTTGATATTGTTAGAGATCAGCAATCAAAGACCCCAAGTC
                    tttacttccattcatt  CT-rich tract
                                      ttttctgttaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacagatcaagaaggttttctctttttgctgcatagcatatttcacacaataaatttgtgaagatttacttccattcatttcttttctgttaaatacagATCAAGAGGGAGATTAAAATACTGCAGAACCTTTGTGGTGGGCCAAATATTGTGAAGTTGCTTGATATTGTTAGAGATCAGCAATCAAAGACCCCAAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
atacaga
- - - - -aagaagg
- - - - - - - - - - - - - - - tgcatag
- - - - - - - - - - - - - - - - - - - - - -tcacaca