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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccttcgtgcatgataaagcataacgtcaaataattggtcagttcatctttgagacgagtaacataagaatcctttttgcatgtgcatcacatattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAAGGACCAGTGGAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTA

Basic information

species Vitis vinifera
transcript Vv17s0000g00610.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g70140.1 (Oryza sativa), 3'ss of exon 2
tccttcgtgcatgataaagcataacgtcaaa--taattgg---tcagttcatctttgagacgagtaacataagaatcctttttgcatgtgcatcacatattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAAGGACCAGTGGAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTA
    | |||  | || |      |  |      || |||    | | |    |||    ||   |||| ||  | || |  || |   | ||    || || |||||||||||| || ||||| ||||  |||||||| ||||||||||| ||||||||||| |||||||| || |||||  ||||||| ||||| |||||  | 
----ttgtgacttatcagttgcgagtttgggattacttgaactttactggcgcttctttactgataac-tacaagtcttgatttctactccaatctatgttgaagGCACCCTAACATTAGCAGCCAAAACGGAGCAATCTGCTTGGACATACTGAAGGACCAATGGAGCCCAGCCCTTACATTGAAGACGGCACTGCTTTCCCTC

upper sequence: Vv17s0000g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G134176_T02 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------------------------------tccttcgtgcatga-taaagcataacgtcaaataattggtcagttcatctttgagacgagtaacataagaatcctttttgcatgtgcatcacatattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAAGGACCAGTGGAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTA
                                                                                                       ||||  |  |||||  | || | |||         ||||  | ||  | |   |      ||    |    |  ||| | ||     |||  || || |||||||||||| |||||||| |||| ||||||||||||||||||||||||||| || ||||||||||| || |||||  ||||||| || ||||||||  | 
gtatgcaagtgtactccctgttacgttatttgtattagtactgatgaattatcatcctggttacataatgtagtcatgtacctacatatgccagttgatacattcctctgatcatgaacagagaacaac-cagcgctgttgggtattttttatccaatttttttagtgcagctctgatttctcca-----atc-tattttgaagGCACCCTAACATCAGCAGCCAAAATGGAGCAATTTGCTTGGACATTCTGAAAGATCAGTGGAGCCCAGCCCTTACCTTGAAGACTGCGCTCCTTTCCCTT

upper sequence: Vv17s0000g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G37620.3 (Glycine max), 3'ss of exon 3
-tccttcgtgcatgataaagca--taacgtcaaataattggtcagttcatctttgagacgagtaacataagaatcctttttgcatgtgcatcacatattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAAGGACCAGTGGAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTA
 |  | | |     ||| ||||  ||| |    |  || ||  | |      ||  |  || |||  || | ||   |||||  |||   | | | ||| |||||| |||||||||||||| ||||||||||| |||||| |||| ||  ||||||||||||||||||| ||||| ||||||||||| ||||| |||||||| 
cttatgcattgcaaatatagcaattaatgcattactatgggaaaatagtctgtttggttgattaatgtatggat---ttttgtgtgtatgttaaacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAAGGACCAGTGGAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTG

upper sequence: Vv17s0000g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G17470.3 (Glycine max), 3'ss of exon 2
---tccttcgtgcatgataaagcataacgtcaaataattggtcagttcatctttgagacgagtaacataagaatcctttttgcatgtgcatcacatattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAAGGACCAGTGGAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTA
   | | | |   || ||||    ||| |    |  || |   | |      ||  |  || |||  |  | ||  ||||||| | ||  | | | ||| |||||| |||||||||||||| ||||||||||| |||||| |||| ||  ||||||||||||||||||| ||||| ||||||||||| ||||| |||||||| 
ttatgcattgcaaat-ataatatttaatgcattactatggcataataatctgtttggttgattaatgtgtggatgttttttgcgtatg--ttaaacattgaagGCATCCTAATATCAGCAGCCAAAGTGGAGCTATTTGCCTGGATATCTTGAAGGACCAGTGGAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTG

upper sequence: Vv17s0000g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G50870.1 (Arabidopsis thaliana), 3'ss of exon 2
tccttcgtgcatgataaagcataacgtcaaataattggtcagttcatctttgagacgagtaacataagaatcctttttgcatgtgc--atcacatattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAAGGACCAGTGGAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTA
  |||  |  |   |  | |||    | | |  ||   | |       ||     | | |||       ||   | |||  ||  |  |||| | ||  |||||| || ||||| || || ||||| || ||||| |||||||| ||  |||| ||||||||||| || || ||||||||||||||||| ||  ||||  | 
ctcttgatagacattttaccatt-tatgacaatatctttgaaactgcattgtgcgctaataaggagtttatttctgttgattgatctgatcaaa-atcaaagGCATCCGAATATTAGTAGCCAAAGCGGTGCAATATGCTTGGATATCTTGAAAGACCAGTGGAGTCCAGCTCTTACTCTGAAGACAGCTCTTGTTTCAATT

upper sequence: Vv17s0000g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ07315 (Selaginella moellendorffii), 3'ss of exon 2
tccttcgtgcatgataaagcataacgtcaaataattggtcagttcatctttgagacgagtaacataagaatcctttttgcatgtgcatcacatattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAAGGACCAGTGGAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTA
      |||  ||  | |||   |    | |  |      | |  |  |||        |   ||    ||| | | | | | | | || |     | ||||| || ||||||||||| |||| |||||| |||||| | |||||||| || |||||||||||||| || || || || ||||| || || |||||| | 
------gtgagtg--agagctcgagaaaagaggaacaaaaaatctagttttttttttcctttgatgctgatcttgtctccttttacttcgc-----ccagGCATCCCAATATCAGCAGCCAAAATGGAGCCATTTGCCTAGACATTCTCAAAGACCAGTGGAGCCCGGCTCTCACCCTCAAGACGGCTCTACTTTCTCTC

upper sequence: Vv17s0000g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ27483 (Selaginella moellendorffii), 3'ss of exon 2
tccttcgtgcatgataaagcataacgtcaaataattggtcagttca-tctttgagacgagtaacataagaatcctttttgcatgtgcatcacatattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAAGGACCAGTGGAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTA
      |||  ||  | ||||  |    | |  |      | |  | | |||        |   ||    ||| | | | | | | | |  |     | ||||| || ||||||||||| ||||  ||||| |||||| | |||||||| || |||||||||||||| || || ||||| ||||| || || |||||| | 
------gtgagtg--agagcacgagaaaagaggaacaaaaaatctagttttttttttttctttgatgctgatcttgtctccttttactttgc-----ccagGCATCCCAATATCAGCAGCCAAAACGGAGCCATTTGCCTAGACATTCTCAAAGACCAGTGGAGCCCGGCTCTCACTCTCAAGACGGCTCTACTTTCTCTC

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|161716905|gb|FC068127.1|FC068127
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGCGGAGCAATTTGCTTGGACATTCTGAA
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|30298293|gb|CB975087.1|CB975087
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|294965161|gb|GW836992.1|GW836992
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|110391172|gb|EC956130.1|EC956130
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|110396526|gb|EC962216.1|EC962216
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|71856652|gb|DT005707.1|DT005707
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAG
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAG
EST: gi|110401583|gb|EC968197.1|EC968197
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGCGGAGCAATTTGCTTGGACATTCTGAA
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|161714263|gb|FC064160.1|FC064160
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGCGGAGCAATTTGCTTGGACATTCTGAA
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|83275178|gb|DV939274.1|DV939274
EST:     GGTACCC-TTTGAGCCTCCAAGAATGCAA-TTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGCGGAGCAATTTGCTTGGACATTCTGAA
genomic: GGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|351028328|gb|FQ427224.1|FQ427224
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|77581774|gb|DV219842.1|DV219842
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|77583170|gb|DV220622.1|DV220622
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|71890757|gb|DT039812.1|DT039812
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|77588446|gb|DV223434.1|DV223434
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGCGGAGCAATTTGCTTGGACATTCTGAA
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|77578362|gb|DV217970.1|DV217970
EST:     CCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGCGGAGCAATTTGCTTGGACATTCTGAA
genomic: CCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
EST: gi|110412172|gb|EC977911.1|EC977911
EST:     ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTG                         GCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA
genomic: ATGGGTACCCTTTTGAGCCTCCAAGAATGCAATTTGCCACGAAAGTTTGgtaaggagaa ... catattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctttgagacgagtaacataagaatcctttttgcatgtgcatcacatattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAAGGACCAGTGGAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTA
           gagtaac  putative branch site (score: 2)
              taacataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccttcgtgcatgataaagcataacgtcaaataattggtcagttcatctttgagacgagtaacataagaatcctttttgcatgtgcatcacatattcaagGCACCCTAATATCAGCAGTCAAAGTGGAGCAATTTGCTTGGACATTCTGAAGGACCAGTGGAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - gcatgat
- - - - - - - - aagcataa
- - - - - - - - - - - - - -caaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatca