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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatataatattgaaaacttatttttctttgttctccttatttttcttggcaactagacagtgttagaacttactttaaatgtatgggaaatggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAGGAAGCTGAAGTACCCAAATACTGGAACCGAGGCTCTTCTAATGGGAATC

Basic information

species Vitis vinifera
transcript Vv16s0022g01840.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0022g01840.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G32910.1 (Glycine max), 3'ss of exon 2
------------aatataatattgaaaacttatttttctttgttctccttatttttcttggcaac-tagacagtgttagaacttactttaaatgtatgggaaatggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAGGAAGCTGAAGTACCCAAATACTGGAACCGAGGCTCTTCTAATGGGAATC
              | |    ||    | | || |   |  ||| |  || || || |||      | |    |||  |    |  ||| |  || || |   |   ||| || |||||||| ||||| |||||||||| | | |||| |||||||||||| |||||||| ||||| ||||| || ||||||||||| ||||| ||||| || 
gtgagttcattgtttttgtcgtttttcagtgatgtaattgggttgttgttgttgttgttgttgttgttgttgttgtgtgtgtgtgttttgagggt-tgtgtggtttggttcagGTGGTCGGCGAGGGCTATAAAGTCATATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCACTTCTCATGGGGATT

upper sequence: Vv16s0022g01840.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G28050.1 (Glycine max), 3'ss of exon 2
---aatataatattgaaaacttatttttctttgttctccttatttttcttggcaactagacagtgttagaacttactttaaatgtatgggaaatggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAGGAAGCTGAAGTACCCAAATACTGGAACCGAGGCTCTTCTAATGGGAATC
   | |    | |||     || || || |   || ||  |    |  ||||    | |   ||||  |    |   ||  | |  ||     |   ||| || |||||||| ||||| ||||| || | | | |||| |||||||||||| |||||||| ||||| ||||| || ||||||||||| ||||| ||||| || 
gtcagttcgttgttgttg--ttgttgttgtcgtttttcagtgacgtaattggattgttgtgtgtgtctgtgtgtgtgtttgaggattgttgtgtttggttcagGTGGTCGGCGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCACTTCTCATGGGGATT

upper sequence: Vv16s0022g01840.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G32900.1 (Glycine max), 3'ss of exon 2
aatataatattgaaaacttatttttctttgttctccttatttttcttggcaactagacagtgttagaacttactttaaatgtatgggaaatggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAGGAAGCTGAAGTACCCAAATACTGGAACCGAGGCTCTTCTAATGGGAATC
           |  |  | ||| || ||     |  | | |    ||      | |   |||| ||    |  ||| |  || || |   |   ||| || |||||||  ||||  ||||| || | | | |||| |||||||||||| |||||||| ||||| ||||| || ||||||||||| ||||| ||||| || 
-----------gtgagttcattgttgttgtcgtttttcagtgactttattggattgtt-gtgtgagtgtgtgttttgagggt-tgtgtggtttggttcagGTGGTCGGAGAGGGGTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGCTTCTCATGGGGATT

upper sequence: Vv16s0022g01840.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G28040.1 (Glycine max), 3'ss of exon 2
---aatataatattgaaaac-ttatttt--tctttgttctccttatttttcttggcaactagacagtgt-tagaacttactttaaatgtatgggaaatggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAGGAAGCTGAAGTACCCAAATACTGGAACCGAGGCTCTTCTAATGGGAATC
   | |  | | |||      ||||| |  | ||||     | || ||   |||     |     || | |     ||        ||  | |    |   ||| || |||||||  ||||| ||||| || | | | |||| |||||||||||| |||||||| ||||| ||||| || |||||||||||  |||| ||||| || 
gtgagttcattgttgttgttgttattgtcgtttttgagtggcgtaattggattgttgtgtcacttgtatgtgtgttttgagggttgtgccttgtgtgtttggttcagGTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATT

upper sequence: Vv16s0022g01840.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G35060.1 (Glycine max), 3'ss of exon 2
aatataatattgaaaacttatttttctttgttctccttatttttcttggcaactagacagtgttagaacttactttaaatgtatgggaaatggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAGGAAGCTGAAGTACCCAAATACTGGAACCGAGGCTCTTCTAATGGGAATC
    | |  |       ||    |  | |  |    || || || || |    |     ||||  |    || |||||  || || |   |   ||| || |||||||| ||||| |||||||||| | | || | |||||||||||| |||||||| ||||| ||||| ||  ||||  | || ||||| ||||| || 
---gtgagttcattgtttttgagtgatgtaattgggttgttgttgtttgttgttgatgtgtgtgtgtgtgtattttaagggt-tgtgtggtttggttcagGTGGTCGGCGAGGGCTATAAAGTCATATGCAATTGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGCGAACTAATGCACTTCTCATGGGGATT

upper sequence: Vv16s0022g01840.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G25370.1 (Arabidopsis thaliana), 3'ss of exon 2
-aatataatattgaaaacttatttttctttgttctccttatttttcttggcaactagacagtgttagaacttactttaaatgtatgggaaatggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAGGAAGCTGAAGTACCCAAATACTGGAACCGAGGCTCTTCTAATGGGAATC
     |   | |  ||| |||  | |     || |  || |    |||      | || | ||||     ||  |||  |  | |  ||       |||||||||||||| || || ||||||||| || | ||||  |||||||| || |||||||| ||||| |||| ||| || ||||| ||  |||| ||||| || 
gtgagtctcactccaaa-ttacgtatagaatttgtaattgtagagcttatacgtttga-attgttgaggttttttttttaattgtttgat------tttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATT

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|351014739|gb|FQ437939.1|FQ437939
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|352791180|gb|FQ480052.1|FQ480052
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|349815436|gb|FQ400591.1|FQ400591
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|349817464|gb|FQ407254.1|FQ407254
EST:     AAAGCCAGAGAGGGCTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|351054833|gb|FQ462863.1|FQ462863
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|351025925|gb|FQ427937.1|FQ427937
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|351016364|gb|FQ446224.1|FQ446224
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|349829904|gb|FQ422217.1|FQ422217
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|110702519|gb|EE081323.1|EE081323
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|349826684|gb|FQ418775.1|FQ418775
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|351023024|gb|FQ430899.1|FQ430899
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|351014737|gb|FQ437937.1|FQ437937
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|351015407|gb|FQ447236.1|FQ447236
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|30305768|gb|CB982562.1|CB982562
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCAGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|110375678|gb|EC940688.1|EC940688
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|351017746|gb|FQ436099.1|FQ436099
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|110698596|gb|EE076278.1|EE076278
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|349832857|gb|FQ422979.1|FQ422979
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|351028263|gb|FQ426164.1|FQ426164
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|351019029|gb|FQ426528.1|FQ426528
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|349830894|gb|FQ418178.1|FQ418178
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|351040197|gb|FQ425283.1|FQ425283
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|351029272|gb|FQ436666.1|FQ436666
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|71857934|gb|DT006989.1|DT006989
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCAGCCAGGGCAATAGAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|71867433|gb|DT016488.1|DT016488
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCAGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|161777281|gb|FC072696.1|FC072696
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
EST: gi|351031438|gb|FQ446641.1|FQ446641
EST:     AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAA                         ATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG
genomic: AAAGCCAGAGAGGACTTCTTCTGAGAAAGTTCCAAAgtgagtttgt ... tggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggcaactagacagtgttagaacttactttaaatgtatgggaaatggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAGGAAGCTGAAGTACCCAAATACTGGAACCGAGGCTCTTCTAATGGGAATC
                     aacttac  putative branch site (score: 2)
                        ttactttaaatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatataatattgaaaacttatttttctttgttctccttatttttcttggcaactagacagtgttagaacttactttaaatgtatgggaaatggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAGGAAGCTGAAGTACCCAAATACTGGAACCGAGGCTCTTCTAATGGGAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - -ttgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - gcaacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgg