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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtctttttttatttgatattctgttttcttctcagtcgattaattctatgttttcttagttttctgtaatgtgataatttcatgtttttctggtttgaatttgattgtgacag

Basic information

species Vitis vinifera
transcript Vv08s0105g00280.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 2
CCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtctttttttatttgatattctgttttcttctcagtcgattaattctatgttttcttagttttctgtaatgtgataatttcatgtttttctggtttgaatttgattgtgacag
 |  || || |    | ||||||| || |  || || |||||||| ||||||||||||||||| ||| |||||||||||||||||| |||||| ||||||||     || | |  | ||| |   || |  |   |   ||||     | || |   | |  |        | || |||  || ||||  |  |||||||   || |      
ACGCCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGTAAGCGCAAGAAAGAGGCACGTCAAGTTCACAAGCGCTCTGCAATTGCCCAGAAGgt-----ttaaatcaaaattttaaattttaattgtttttttaacatagttttattgcaataattc------taattattggat-ttttgttaatttgaatggaatag------

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G00490.1 (Glycine max), 5'ss of exon 2
CCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtctttttttatttgatattctgttttcttctcagtcgattaattctatgttttcttagttttctgtaatgtgataatttcatgtttttctggtttgaatttgattgtgacag
 | ||| || |    | ||||||| || |  || || |||||||| ||||||||||||||||| ||| |||||||||| ||||||| |||||| ||||||||    ||  ||   | ||| |||||| |  |  ||   ||  ||  |  |  |  || || |||  | | | || |||  || ||||  |  ||||||||  |  |      
GCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAACGCTCTGCAATTGCCCAGAAGgt----ttaaatcaaaaattttgtttt-taattggtt--tttgtttaacctagttcta-ttgtcttaattctaattattcgat-ttttgttaatttgaattgaacag------

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 2
CCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtctttttttatttgatattctgttttcttctcagtcgattaattctatgttttcttagttttctgtaatgtgataatttcatgtttttctggtttgaatttgattgtgacag
 | ||| || |    | ||||||| || | ||| || |||||||| ||||||||||||||||| ||| |||||||||| || |||  |||||| ||||||||     || | |  |  || |  ||| |    | | | ||  || ||   |   |   || |||  | | | || |||     ||||  |  ||| |||   |  |      
GCGTCACAGAAGAGACTATGGCTACCGTCTTGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAACGTTCTTCAATTGCCCAGAAGgt-----ttaaatcaaagttttagttttt----aattgcttttttttaacctagttgtattgtcttaattctaatcatt--gatttttgttaattttaatggaacag------

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 2
CCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtctttttttatttgatattctgttttcttctcagtcgattaattctatgttttcttagttttctgtaatgtgataatttcatgtttttctggtttgaatttgattgtgacag
  | || |||||| |  |||| |||||||  ||||| |||||| | ||||||||||| ||||| |||||||||||||||| |||    || ||||| |||||  ||                  |||||||||  |||  |  ||| ||    | |||| || || | |  ||||       | || ||||| |||   | | ||||      
TTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGCACTCCACCATGGCTCAAAAGgttctt----------------actttcttctccttcgtcttcttccat----ttttagcttccttttac-tgat-------tcttcttctgcttttgctctaattgcag---

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|351034903|gb|FQ458260.1|FQ458260
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|37189315|gb|CF608664.1|CF608664
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|110388463|gb|EC953218.1|EC953218
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|351034907|gb|FQ458264.1|FQ458264
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|161706371|gb|FC055477.1|FC055477
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|110689931|gb|EE066589.1|EE066589
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|349827619|gb|FQ422487.1|FQ422487
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|351012282|gb|FQ429967.1|FQ429967
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|351053282|gb|FQ459150.1|FQ459150
EST:     GCAAGAAAGAGGCTCGTGGAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|110691373|gb|EE069403.1|EE069403
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|351025564|gb|FQ426380.1|FQ426380
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|71875347|gb|DT024402.1|DT024402
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|110686904|gb|EE063847.1|EE063847
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|351035636|gb|FQ463481.1|FQ463481
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|349827505|gb|FQ422373.1|FQ422373
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|351056948|gb|FQ443575.1|FQ443575
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGGTGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|351032431|gb|FQ458796.1|FQ458796
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|351049548|gb|FQ429170.1|FQ429170
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|349830525|gb|FQ416835.1|FQ416835
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|77588634|gb|DV223535.1|DV223535
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|351049014|gb|FQ431558.1|FQ431558
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|351056833|gb|FQ443460.1|FQ443460
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|71875464|gb|DT024519.1|DT024519
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
EST: gi|161720669|gb|FC070613.1|FC070613
EST:     GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAG                         GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG
genomic: GCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtcttttttt ... attgtgacagGCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGCGCTCTGAAATTGCTCAGAAGgtctttttttatttgatattctgttttcttctcagtcgattaattctatgttttcttagttttctgtaatgtgataatttcatgtttttctggtttgaatttgattgtgacag

- - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG