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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagatagctaatgacccggttaggtggagattgctgggggagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA

Basic information

species Vitis vinifera
transcript Vv10s0003g03710.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AC177936.6_FGT008 (Zea mays), 3'ss of exon 4
---------tagatagctaat-gacccggttaggt--ggagattgctgggggagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA
          |||    ||||  |    | |  ||  |    || |     || || |||| |  | |  |   || |  |  |   |||||| | |  |||       ||||| || || ||  | |||||||||||| | |||||||| || || ||| | || ||| |||||||||| ||||||||||  |  ||||||||||| ||||
gtgacacttcagaatattaattaatttagctgtgtatgttatttaccttacgacaacttgaccccctttaacctttggggttcat--ccatgtctctcattt-------cagCTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTAATAGACCGGGAGTACCTGGAGCGGGACAGGAGTAACCCCCAGATCTACA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 16
---------tagatagctaat-gacccggttaggtg-gagattg--ctgggggagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA
          |||   |||||  |    | |  ||  |  ||||  ||   ||  || ||||||  | |  ||   |||  |   |  ||||||   |  |||       ||||| || || ||  | |||||||||||| | |||||||| || || ||| | |||||| |||||||||| ||||| ||||  |  ||||||||||| ||||
gtaactcttcagaatactaattaatttagctgcgtatgttattgacctcacggctaacttgaaccccctttaaccgttgggtttcat-ccatgtccctcattt-------cagCTCAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTGATCGACCGGGAGTACCTGGAGCGCGACAGGAGTAACCCCCAGATCTACA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 16
------------tagatagctaatgacccggttaggtggagattgctgggggagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA
            || |||   || ||| |  ||  |  |  | |  ||   ||   |  |   | ||||     |||  || |   |     || || ||||  |   |||||| ||||| |||||||| |||||||||||||| |||||||||||||||||||| ||||||||||| |||||| ||||||| | ||| || || |||||||
ttctgttgtgattaaataaa-aacgacacaattctgatgctacttttgtctgattttcggggatacata-----tttactttaggtat----ttattatttt--ttgtacagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTCATTGACAGGGAGTATCTAGAGAGGGACAAGAGCAATCCTCAAATATACA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 16
tagatagctaatgacccggttaggtggagattgctgggggagaatttgaacttcata---gaagatttgattgaaaaaccatgtttttgtt-ttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA
    |   |  |||     | |    || |    |  |     | ||     | ||    |  ||| | ||    |    | || ||| || ||  |    ||||| ||||| |||||||| |||||||||||||| |||||||||||||||||||| ||||||||||| |||||| ||||||| | ||| || || |||||||
----tctgttgtgattaaataaaaacgacacacttctgatgctacttttgtctgattttcggggatataatactcactttaggtatttattattttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTCATTGACAGGGAGTATCTAGAGAGGGACAAGAGCAATCCTCAAATATACA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 16
------tagatagctaatgacccggttaggtggagattgctgggggagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA
      || |   | | ||| |   || | |  ||| || |          ||||   | |   || | |   || |  ||     |||||   |||    ||||||| |||||||||||||| |||||||| |||||||||||||| |||||||| || ||||||||||| || ||| | ||||| |||||||| || |||||||
gttgtgtacaatacaagtgatctcttttgatacagactgttttctctctgattga---taagttaatactaatttaaggaagtgaattttt---ttgtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGACAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 17
------tagatagctaatgacccggttaggtggagattgctgggggagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA
      | |    | | | | |   || | || ||| || |    |    | |||   | |    |    ||||| ||  |   || |||| ||    |||| ||||| |||||||||||||| |||||||| |||||||||||||| |||||||| || || |||||||| || ||| | ||||| |||||||| || |||||||
cttatgttgtgtacaagttatctcttttgatgcagactgttttctg----tctgattgttaagataatactgatttaaggaa-gtgatttttttcatgtgaa-cagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGATAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: PP1S204_102V6.1 (Physcomitrella patens), 3'ss of exon 15
---------------------------------------------------------------------------------tagatagctaatgacccggttaggtggagattgctgggg-gagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA
                                                                                 ||  |   ||     |||   |  |     |||||     ||    |||    | ||      ||   ||    |  |   |   |  ||  ||    ||||| ||||||||||| || ||||||||| ||||||| || ||||| ||||| |||||  ||||||| || ||  ||||||||  |||||| || |||||||
gtaatacgttcattctcggaaattgtgccttcatgttttgggtgtggacacgcaagttttttattttattttattttattttatttttttagccctccgtggatatctcacttgcttatttgatttcttgcttataattctttgttatttttgcgactccaatgactcgttgaattttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTGATCGATCGGGAGTATCTGGAAAGGGACAAAGCCAACCCTCAAATATACA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: PP1S70_181V6.1 (Physcomitrella patens), 3'ss of exon 15
-------------------------------------------tagatagctaatgacccggttaggtggagattgctgggggagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA
                                            |  |    ||     || | | ||| ||  |||||     ||| ||     |   |   | |||  |||       | |  | || | | |     ||||| ||||||||||| || |||||||| ||||||||||| || || ||| | || ||| |||||||||| ||  ||||||||  ||| || ||||| ||||
gtgaatatttcatacctcgaattattatccagaatttcggattcacttctgcaagtcatcgatgatgtgtag--tgctgttattgaaattctgtatttcaagtgttttttttgttgttaaacgcatgtgatgttaaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTGATTGACCGGGAGTACCTTGAAAGGGACAAAGCCAATCCTCAGATCTACA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: EFJ14633 (Selaginella moellendorffii), 3'ss of exon 16
tagatagctaatgacccggttaggtggagattgctgggggagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA
                                     |  ||   | |    |  | |||  |      ||      || | ||| || ||    | ||||| || || || ||||||||||| || ||||||||| | || || ||||| |||||| | |||||| | ||||| ||||| |||||||| ||| ||||||
-------------------------------------gtaaggcctggctgctgttggaatgtggtgccgacgctgtatatgttttttgtgtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTGATCGACCGCGAGTACTTGGAGCGAGACAAGAACAACCCTCAGGTATACA

upper sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: EFJ26297 (Selaginella moellendorffii), 3'ss of exon 16
tagatagctaatgacccggttaggtggagattgctgggggagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA
                                     |  ||   | |    |  | |||  |      ||      || | ||| || ||    | ||||| || || || ||||||||||| || ||||||||| | || || ||||| |||||| | |||||| | ||||| ||||| |||||||| ||| ||||||
-------------------------------------gtaaggcctggctgctgttggaatgtggtgccgacgctggatatgttttttgtgtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTGATCGACCGCGAGTACTTGGAGCGAGACAAGAACAACCCTCAGGTATACA

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|110358187|gb|EC922223.1|EC922223
EST:     CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAG                         CTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC
genomic: CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAGgtaactggat ... gatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC
EST: gi|71878599|gb|DT027654.1|DT027654
EST:     CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAG                         CTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC
genomic: CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAGgtaactggat ... gatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC
EST: gi|110357401|gb|EC920914.1|EC920914
EST:     CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAG                         CTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC
genomic: CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAGgtaactggat ... gatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC
EST: gi|30126630|gb|CB911969.1|CB911969
EST:     CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAG                         CTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC
genomic: CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAGgtaactggat ... gatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC
EST: gi|110417958|gb|EC984063.1|EC984063
EST:     CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAG                         CTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC
genomic: CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAGgtaactggat ... gatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC
EST: gi|71879873|gb|DT028928.1|DT028928
EST:     CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAG                         CTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC
genomic: CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAGgtaactggat ... gatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC
EST: gi|30133901|gb|CB919240.1|CB919240
EST:     CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAG                         CTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC
genomic: CGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAGgtaactggat ... gatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA
                                         ttttgat  putative branch site (score: 4)
                atttgattgaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagatagctaatgacccggttaggtggagattgctgggggagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA

- - - gctaatg
- - - - - - - - - - - ggtggag
- - - - - - - - - - - - - - - - - -gggggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - atagaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaccat