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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGAGAATCTCATGGAGGTGGTGTTGGTTGCATAATTGATGGATGTCCTCCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgacttttaaggacttggctttgacttagagatggaagtctatccttggtttcatgttagaatttgtctggtttttgatcaatgaatgtttaaac...

Basic information

species Vitis vinifera
transcript Vv13s0019g04190.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 5'ss of exon 2
ATGGAGAATCTCATGGAGGTGGTGTTGGTTGCATAATTGATGGATGTCCTCCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgacttttaaggac--ttggctttgacttagagatggaagtctatcct---tggtttcatgttag---aatttgtctggtttttgatcaa---tgaatgtttaaac----------------------------------------------
||||||| ||||||||||| |||||||||||| ||||   |||||| || ||  |  | || || || || || ||||||||| |||| || ||  | ||||   |  |||  ||   |  ||   | ||   |       |   ||| ||       |  | |||  |    |||    ||    | |     |   ||| ||||                                                   
ATGGAGAGTCTCATGGAGGCGGTGTTGGTTGCGTAATCAGTGGATGCCCACCCAGAATCCCACTTACTGAAGCAGATATGCAAGTAGAACTCGACCGGAGgtttgtctcttgaaaaatccattatttctgtgctgacagctggcttctgtcaaaaacaggattatgcaaatgcaatcctgctaacctcttgcagaatatgattgttatgttacattacaccataatgttaactgacataaaattttgattatcacag

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G35560.1 (Glycine max), 5'ss of exon 2
ATGGAGAATCTCATGGAGGTGGTGTTGGTTGCATAATTGATGGATGTCCTCCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgacttttaaggacttggctttgacttagagatggaagtctatccttggtttcatgttagaatttgtctggtttttgatcaatgaatgtttaaac----
|||||||||| |||||||| ||||||||||| || ||||||||||||||||||| |||||| ||| | || |||||||||||| | |||||||| |||||||   || | | | |   | |  ||||  |||    || ||| |   | | | ||   ||   |  | |||   ||||   ||  |||   |  |   |     
ATGGAGAATCGCATGGAGGAGGTGTTGGTTGTATTATTGATGGATGTCCTCCTCACCTTCCTCTCTCCGAAGCTGATATGCAATTGGATCTTGACAGAAGgtgcttg-cctatgaaatcatctctttatcttc---attgaactgcttgcattgtgggataaaaacacttgggaggttgaagagaaatactttataggatagtt

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA20G31980.1 (Glycine max), 5'ss of exon 2
ATGGAGAATCTCATGGAGGTGGTGTTGGTTGCATAATTGATGGATGTCCTCCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgacttttaaggacttggctttgacttagagatggaagtctatccttggtttcatgttagaatttgtctggtttttgatcaatgaatgtttaaac-------
|||| ||||| |||||||| |||||||||||  | |||||||||||||||||||||||||| ||| | || |||||||||||| | |||||||| |||||||   || | | | |   | |  ||||  |||    || |||  |||    |  ||    |  | ||    | |||   ||||  |   |   |||| |        
ATGGGGAATCACATGGAGGAGGTGTTGGTTGTGTTATTGATGGATGTCCTCCTCGCCTTCCTCTCTCTGAAGCTGATATGCAAGTGGATCTTGACAGAAGgtgtttg-cctctgaaatcatctctttatcttc---attgaa--ctacttgta-ttgtgggagaaaaacactttggacgttgaagagaaatactttataggatagtt

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT1G48850.3 (Arabidopsis thaliana), 5'ss of exon 2
ATGGAGAATCTCATGGAGGTGGTGTTGGTTGCATAATTGATGGATGTCCTCCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgacttttaaggacttggctttgacttagagatggaagtctatccttggtttcatgttagaatttgtctggtttttgatcaatgaatgtttaaac
 ||||||||| |||||||| || |||||||| || |||||||| |||||||||||  |||| || || ||  ||||| ||||| | ||||| |||||||||||  |       ||| |    ||| | |||     ||  ||    ||| || | || |  |     ||||  |  ||                      
TTGGAGAATCACATGGAGGAGGAGTTGGTTGTATCATTGATGGTTGTCCTCCTCGTATTCCACTTACTGAATCTGATTTGCAATTCGATCTCGATAGAAGgtattttgagg--aagaagaaagctcttact-----atataatatgatcgtttgatttacatgttggtttgctttattag--------------------

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|352790897|gb|FQ477345.1|FQ477345
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATCGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|71880899|gb|DT029954.1|DT029954
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATCGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|71877721|gb|DT026776.1|DT026776
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATCGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|71863219|gb|DT012274.1|DT012274
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATCGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|352778035|gb|FQ467088.1|FQ467088
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|71855293|gb|DT004348.1|DT004348
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|71861705|gb|DT010760.1|DT010760
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATCGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|71879200|gb|DT028255.1|DT028255
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATCGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|71880874|gb|DT029929.1|DT029929
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATCGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|352776661|gb|FQ465459.1|FQ465459
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|352785537|gb|FQ475540.1|FQ475540
EST:     CCACACCTTCCCCTCACAGAGGCTGATATGCAAATCGATCTTGATAGAAG                         GAGGCCAAGACAGAGCCGAATTA
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTA
EST: gi|352777956|gb|FQ467009.1|FQ467009
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|351024445|gb|FQ426254.1|FQ426254
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATCGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|352778092|gb|FQ467145.1|FQ467145
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|352763986|gb|FQ467556.1|FQ467556
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
EST: gi|352768213|gb|FQ467352.1|FQ467352
EST:     CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAG                         GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG
genomic: CCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgact ... ttgtgtctagGAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGAGAATCTCATGGAGGTGGTGTTGGTTGCATAATTGATGGATGTCCTCCTCGCCTTCCCCTCACAGAGGCTGATATGCAAATAGATCTTGATAGAAGgtaactgacttttaaggacttggctttgacttagagatggaagtctatccttggtttcatgttagaatttgtctggtttttgatcaatgaatgtttaaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT