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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtaccttttgaaatagagggaaaatttccccaattattactttggatgcagcatccttatggatagtattggatttggaatacaaatgatacacctttagtagctcatacttttaacaacttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATGGCTGGTGCAGCTCAGACTGTTAAAAAG

Basic information

species Vitis vinifera
transcript Vv19s0085g00880.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0085g00880.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G17450.1 (Glycine max), 3'ss of exon 9
gtattgtaccttttgaaatagagggaaaatttccccaattattactttggatgcagcatccttatggatagtattggatttg-gaatacaaatgatacacctttagtagctcatacttttaacaacttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATGGCTGGTGCAGCTCAGACTGTTAAAAAG
                                             ||  | | |    |  || |    || | |    ||| ||||  || |||  | |||  |  ||   | | | | |||  |||||| ||||||||||||||||||| |||||||| ||||| || || ||||| |||||||||||| ||||| | || |||||||| 
--------------------------------------------gttctgttaccatgttattttacgaagcaattaccttgtgaatgtaattga-gcgcctgaaaaag---aaattatcaac--cttatttagGTAAGGAAGATCACATTCACAGGCTCGACAGCAGTTGGGAAGAAATTGATGGCTGGTTCAGCTGAAACAGTTAAAAAA

upper sequence: Vv19s0085g00880.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 9
gtattgtaccttttgaaatagagggaaaatttccccaattattactttggatgcagcatccttatggatagtattggatttggaatacaaatgatacacctttagtagctcatacttttaacaacttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATGGCTGGTGCAGCTCAGACTGTTAAAAAG
                                          | || ||     |  ||  ||| | |    |||   ||  ||||  || ||| ||| ||     ||   | | | | |||  |||||| ||||||||||||||||||| |||||||| || ||||| || ||||| |||||||||||| ||||| | || |||||||| 
-----------------------------------------gttctgtgaccatattatt-ttacgaagca-attaccttgtgaatgtaattga-acatctgagaaag---aaattatcaac--cttatttagGTAAGGAAGATCACATTCACAGGCTCGACGGCTGTTGGGAAGAAATTGATGGCTGGTTCAGCTGAAACAGTTAAAAAA
















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|349825250|gb|FQ417971.1|FQ417971
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|110688026|gb|EE066106.1|EE066106
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCGACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|351042224|gb|FQ442691.1|FQ442691
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGTAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|30302041|gb|CB978835.1|CB978835
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|351028680|gb|FQ446353.1|FQ446353
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|29785203|gb|CB341997.2|CB341997
EST:     CAAGTCGGCAG                         GTAAGGAAGATCACATTTATCAGGCTCAACAGCTGTCGGAAAGAAGTTGAT
genomic: CAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTA-CAGGCTCAACAGCTGTCGGAAAGAAGTTGAT
EST: gi|351022813|gb|FQ428722.1|FQ428722
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|349827719|gb|FQ422587.1|FQ422587
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|110712816|gb|EE088195.1|EE088195
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|77587321|gb|DV222801.1|DV222801
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|349823645|gb|FQ415055.1|FQ415055
EST:     TCTTTGGAAATGCTCCTGAAATGGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCA
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCA
EST: gi|33407740|gb|CF213367.1|CF213367
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGT
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGT
EST: gi|161718701|gb|FC066339.1|FC066339
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCGACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|349832930|gb|FQ423052.1|FQ423052
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|34543124|gb|CF511356.1|CF511356
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|110393201|gb|EC958271.1|EC958271
EST:     TTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCGACAGCTGTCGGAAAGAAGTTGATG
genomic: TTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|110377270|gb|EC942333.1|EC942333
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|110685428|gb|EE062138.1|EE062138
EST:     CTTTTGGAA-TGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGA-GATCACATTTACAGGCTCA-CAGCTG
genomic: CTTT-GGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTG
EST: gi|349824141|gb|FQ417528.1|FQ417528
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACA
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACA
EST: gi|29785173|gb|CB341929.2|CB341929
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|351012714|gb|FQ430277.1|FQ430277
EST:     TCTTTGGGAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCA
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCA
EST: gi|349828464|gb|FQ417206.1|FQ417206
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCA
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCA
EST: gi|30251721|gb|CB969454.1|CB969454
EST:     TTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|351028364|gb|FQ427260.1|FQ427260
EST:     TCTTTGGAGATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
EST: gi|351016508|gb|FQ423935.1|FQ423935
EST:     CTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGGCA-GTCGGCAA                         GTAAGGAAGATCACATTTAC
genomic: CTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTG-CAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTAC
EST: gi|351033667|gb|FQ462197.1|FQ462197
EST:     TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAG                         GTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG
genomic: TCTTTGGAAATGCTCCTGAAATTGGGGATGCTTTACTTGCAAGTCGGCAGgtattgtacc ... acttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggaatacaaatgatacacctttagtagctcatacttttaacaacttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATGGCTGGTGCAGCTCAGACTGTTAAAAAG
                                     ttttaac  putative branch site (score: 2)
                                              cttattc  putative PPT
                                     ttttaacaacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtaccttttgaaatagagggaaaatttccccaattattactttggatgcagcatccttatggatagtattggatttggaatacaaatgatacacctttagtagctcatacttttaacaacttattcagGTAAGGAAGATCACATTTACAGGCTCAACAGCTGTCGGAAAGAAGTTGATGGCTGGTGCAGCTCAGACTGTTAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA