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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttgtggctgtgttcaatatgggatttgtccaataccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcag

Basic information

species Vitis vinifera
transcript Vv06s0004g00240.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 11
TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtg-atacttgtgg-ctgtgttcaatatgggatttgtcc-aataccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggact--tgaattgattgcag-----------
|||||||||||| |||||||| ||||| ||||||||||| |||||||| ||  | |  || || |||||||||||||  || || ||||||||| | |||||  | |    ||  ||   ||    || |  ||||| | | |    |          | || ||| ||||    |  ||       |  |    || ||       | || |||      | |  || |||| |  || ||   |  || ||  |||||             
TGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTCTGAGACTGGCAGCTAGAGTTGACGCCATCAAGGACAACCTGGAGAATGATGAGCAGAAGgtttacaaccatgatctactttattcattgtttttgttcgagtgttctataaacctcatctctcaaaagttctgtttttgtgcctgctactatgtatatgggttagaaatgaccatctcgaatttgttgtcctttctaattgacttgttgtatgtattgcttgaactttttag

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G083716_T03 (Zea mays), 5'ss of exon 10
TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttgtggctgtgttcaatatgggatttgtccaataccttgagttttggttttcccaatagtttg-aatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcag
 ||||||||||| |||||||| ||||| |||||||||||  || | |||||  | || || || ||||||||||| || || || || || ||| | ||||| | |       |||   ||     |  |||  |   | |    |||  | |       ||| ||     || | ||||  ||  ||||||     |   | ||  ||  | |    |||                                     
CGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaaaatctgcaatcc---cgtaattcatttgaaa----gaggatggagg----caacagagcacaaccttgct--ataggttcaactatggctgacattctgaactgacattag-------------------------------------

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 10
TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttgtggctgtgttcaatatgggatttgtccaa-taccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcag
||| |||||||| |||||||| |||||||| |||||||| ||||||||||| |||||||||||||| |||||||| |  |||||||||||||| ||||| ||||     ||   | | ||  ||||||      |  || |  | ||  | |||   |      |  ||||  |  ||   ||||      |    |||    | |||   |   | | | || | ||    | ||| | |  || ||||  ||||||
TGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtga-----gtcatt-tatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaaca-tggtcatgacttcaaaattgtgtttaattt-ttgcag

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA08G18760.3 (Glycine max), 5'ss of exon 10
TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttgtggctgtgttcaatatgggatttgtccaa-taccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcag-------
    |||||||| |||||||| |||||||| |||||||| ||||||||||| |||||||||||||| |||||||| |  |||||||||||||| ||||| ||||     ||   | | ||  ||||||      |  || |  | ||  | |||   |      |  ||||  |  ||   ||||      |    |||    | |||   |   | | | || | ||    | ||| | |  || ||||  ||||||       
----GAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAGTGA-

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 10
TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttgtggctgtgttcaatatgggatttgtccaataccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcag
||| ||||| || ||||| || |||||||| |||||||| ||||||||||| |||||||||||  | |||||||| |  |||||||||||||| ||||| ||||     ||   | | ||  ||||||      | |||     |  | | | ||  |     |  ||||  |  ||   ||||  |   |    ||     |  |   |     ||  ||| | ||    | ||| | |  || ||||| ||||||
TGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtga-----gtcatt-tatttgatatggagagaatacaagtttcttggatgttgtgatatttttgttttgggtgctgggaaatgcttctgactgttgctttcaactcaactcc--tagcgtggtcatgacttcaaaattgtgtttaattg-ttgcag

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttgtggctgtgttcaatatgggatttgtccaataccttgagttt-tggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcag
|||||||||||| ||||| || |||||||| |||||||| ||  | ||||| |||||||| |||||||||||||| || ||||| |||||||| |||||||||||            |     |      |||  | |||  ||||   ||   |  ||  |||   |||    |||    |                                                                            
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggcaaaatcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttc--ccatctctag---------------------------------------------------------------------------

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 11
TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttgtggctgtgttcaatatgggatttgtccaataccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcag
||| |||||||| |||||||| |||||||| |||||||| ||  | ||||| || ||||| |||||||| || | |||||||||||||||||| |||||||| |  |        || ||||      |||||    ||  | |  |  || |||||  | ||   ||||     || ||| |   || |                                                                   
TGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAGAAAAGgtaaatcaatcaa--gtcttca------gattt---taactcatgaaccttcggtttctctaac--tttgc----tgatgattccctttag------------------------------------------------------------------

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: EFJ36935 (Selaginella moellendorffii), 5'ss of exon 10
TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtga---tacttgtggctgtgttcaatatgggatttgtccaataccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcag
|||||| ||||| || ||||| ||||| ||     |||| || |||||  |    ||||| |||||||||||||| || ||||| ||||| ||| |||||||||    ||||  |   |  |||  | ||  |   ||| | |||||   ||||  |                                                                                                       
TGTTGAAGAAGGCATCGTTGTCGGTGGGGGAATTGCTCTTCTAAGACTGTCTAGCAAGGTTGATGCCATCAAGGATACCCTTGAGAATGACGAGCAAAAGgtgaggccacttcagaaagctttccctctgaaa---gtcaattacct---gtttcag-------------------------------------------------------------------------------------------------------

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: EFJ33580 (Selaginella moellendorffii), 5'ss of exon 10
TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttgtggctgtgttcaatatgggatttgtccaataccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcag
|||||| ||||| || ||||| ||||| ||     |||| || |||||  |    ||||| |||||||||||||| || ||||| ||||| ||| |||||||||       |||    ||||  |   | |||| ||    |  |||   |    |  |      |||| |                                                                                      
TGTTGAAGAAGGCATCGTTGTCGGTGGGGGAATTGCTCTTCTAAGACTGTCTAGCAAGGTTGATGCCATCAAGGATACCCTTGAGAATGACGAGCAAAAGgtga-------ggccac-ttcagaa--agctttgaccctccctctgaaagtcaagtacct-----gtttcag-------------------------------------------------------------------------------------

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|33401980|gb|CF207607.1|CF207607
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|26259554|gb|CA810617.1|CA810617
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|110363904|gb|EC927535.1|EC927535
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGTTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|351022937|gb|FQ428846.1|FQ428846
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|351030401|gb|FQ432339.1|FQ432339
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|110419196|gb|EC985406.1|EC985406
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|37188314|gb|CF607663.1|CF607663
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|110688028|gb|EE066108.1|EE066108
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|34547567|gb|CF515799.1|CF515799
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|351034062|gb|FQ447979.1|FQ447979
EST:     CCTCANAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAG-AAA-G                         GTTGGAGCTGATATTGTCCAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|34547481|gb|CF515713.1|CF515713
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|110362655|gb|EC926202.1|EC926202
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|110362851|gb|EC926408.1|EC926408
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|110420169|gb|EC986432.1|EC986432
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|34549838|gb|CF518070.1|CF518070
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|33401795|gb|CF207422.1|CF207422
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
EST: gi|351022922|gb|FQ428831.1|FQ428831
EST:     CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAG                         GTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT
genomic: CCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttg ... ttgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttgtggctgtgttcaatatgggatttgtccaataccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA