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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcaattaccacgtttattggacattaatccatgtggttgaggtccttacccctgatggttttcatttttcttaatgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAAGGATTGTTAACAACAAGATG

Basic information

species Vitis vinifera
transcript Vv13s0019g02360.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA02G41850.1 (Glycine max), 3'ss of exon 15
gtatgtttcaattaccacgtttattggacattaatccatgtggttgaggtccttacccctgatggttttcatttttcttaatgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAAGGATTGTTAACAACAAGATG
||||  |    ||  ||  |||||| |  || |||| ||    || ||||  ||        |  | |  | ||  |||   | ||||||||||||||| ||||| || ||||||||||||||||||||||| |||||||| ||||||||||||||||||||
gtataatattgtttgcat-tttatttgtaatcaatctattgcattaaggttgttgatt----tattatgtaattcccttctggttgaatagGTTGGAATTAGTACGAGCAGGATTCATGCTCGAGGTCCAGTAGGAGTTGAGGGATTGTTAACAACAAGATG

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 18
gtatgtttcaattaccacgtttattggacattaatccatgtg-gttgaggtccttaccc---ctgatggttttcatttttcttaatgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAAGGATTGTTAACAACAAGATG
||||| |  | |    || ||  ||  | | | || |   |  | | | ||| ||        | ||  || |||| |   |   |  |  ||||||||||||||||||||| |||||||||||||| |||||||| |||||||| |||||||||||||| |||||
gtatgat--attctttacattcttttaataatcattctcttatgctaaagtcattgatttaattcataattctcatgtcattggctttt--atagGTTGGAATAAGTACAAGCAGGATTCATGCTCGGGGTCCAGTAGGAGTTGATGGATTGTTAACAACCAGATG

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA14G07120.1 (Glycine max), 3'ss of exon 15
gtatgtttcaattaccacgtttattggacattaatccatgtggttgaggtccttacccctgatggttttcatttttcttaatgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAAGGATTGTTAACAACAAGATG
||||  |     |  ||  ||||||    || |||| ||    || ||||  ||        |  | |  | ||  |||   | ||||||||||||||| ||||| || ||||||||||||||||||||||| || ||||| ||||||||||||||||||||
gtataatattggttgcat-tttatt----atcaatctattgcattaaggttgttgatt----tattatgtaattcccttctggttgaatagGTTGGAATTAGTACGAGCAGGATTCATGCTCGAGGTCCAGTAGGTGTTGAGGGATTGTTAACAACAAGATG

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT3G55610.1 (Arabidopsis thaliana), 3'ss of exon 18
------gtatgtttcaattaccacgtttattggacat-taatccatgtggttg---aggtccttacccctga-tggttttcatttttcttaatgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAAGGATTGTTAACAACAAGATG
          |    | ||||||    |||   | || ||| |||      ||   | ||    |    | | |||      |  ||  |  |  || |||||| |||||||| ||||| ||||||||||| || |||||||| |||||||||||||| || |||||||||||
gtagggaagagagagagttaccaataatatcacatatataaaccaaacaaatggagaagtgtcaatgaataaatggccaatgtgatttgttcttatgtatagGTGGGAATAAGCACAAGCAGGATTCATGCCCGTGGTCCAGTTGGAGTTGAAGGATTATTGACAACAAGATG

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|110364352|gb|EC923948.1|EC923948
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|29783366|gb|CB349487.2|CB349487
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|30297817|gb|CB974611.1|CB974611
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|110427351|gb|EC993787.1|EC993787
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GATGGAATAAGTACAAGTAGGATTCATG
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATG
EST: gi|33402185|gb|CF207812.1|CF207812
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|33402196|gb|CF207823.1|CF207823
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|110377214|gb|EC942273.1|EC942273
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTAGGAATAAGTACAAGTAGGATTCATG
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATG
EST: gi|110365796|gb|EC929255.1|EC929255
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|33402539|gb|CF208166.1|CF208166
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|32461077|gb|CD802251.1|CD802251
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|110362804|gb|EC926359.1|EC926359
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|110382148|gb|EC938618.1|EC938618
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|27585130|gb|CB007825.1|CB007825
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|110375487|gb|EC940476.1|EC940476
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATG
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATG
EST: gi|110420384|gb|EC986656.1|EC986656
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|110388887|gb|EC953685.1|EC953685
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|33402105|gb|CF207732.1|CF207732
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|29783302|gb|CB349405.2|CB349405
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|110414936|gb|EC980800.1|EC980800
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAA
EST: gi|110421820|gb|EC988122.1|EC988122
EST:     ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAG                         GTTGGAATAAGTACAAGTAGGATTCATG
genomic: ATGCTAGCACAAGATTTTGTGATGGGGCTCGTTTTGGACTTGGGGCCGAGgtatgtttca ... tgctgaatagGTTGGAATAAGTACAAGTAGGATTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtggttgaggtccttacccctgatggttttcatttttcttaatgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAAGGATTGTTAACAACAAGATG
                             ttttcatttttcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttcaattaccacgtttattggacattaatccatgtggttgaggtccttacccctgatggttttcatttttcttaatgctgaatagGTTGGAATAAGTACAAGTAGGATTCATGCTCGAGGTCCAGTCGGAGTTGAAGGATTGTTAACAACAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG