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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcatcatgatattgagcattggttgatatatcataacagtaccattcactagttggcctattccatttagtatttttattgttgttacctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCCATCTCCTGGTCAAGGATTTTCCCTG

Basic information

species Vitis vinifera
transcript Vv14s0006g01790.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g49600.2 (Oryza sativa), 3'ss of exon 2
aatcatcatgatattgagcattggttgatatatcataacagtaccattcactagttggcctattccatttagtatttttattgttgttacctgtttg--cagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCCATCTCCTGGTCAAGGATTTTCCCTG
       ||| | |  |  ||  ||    |     | ||| ||| ||  |   |||  | |  ||||||   ||     |  ||   | | |  | |  ||||||||| |  |  | ||||||| ||||||||||||||| ||||| ||||| ||||| ||||| ||||| ||||| |
-----aaatgctctaaaatatgcgtgtccaaggtcttacattac-atgtaagtgtttccattctccattatctaaaaaaaaagtgtatccattctggaacaggaagATGTTAATCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG

upper sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g49600.3 (Oryza sativa), 3'ss of exon 2
aatcatcatgatattgagcattggttgatatatcataacagtaccattcactagttggcctattccatttagtatttttattgttgttacctgtttg--cagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCCATCTCCTGGTCAAGGATTTTCCCTG
  |    ||| | |  |  ||  ||    |     | ||| ||| ||  |   |||  | |  ||||||   ||     |  ||   | | |  | |  ||||||||| |  |  | ||||||| ||||||||||||||| ||||| ||||| ||||| ||||| ||||| ||||| |
-ctgtaaatgctctaaaatatgcgtgtccaaggtcttacattac-atgtaagtgtttccattctccattatctaaaaaaaaagtgtatccattctggaacagGAAGATGTTAATCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG

upper sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g49610.1 (Oryza sativa), 3'ss of exon 2
aatcatcatgatattgagcattgg-ttgatatatcataacagtaccattcactagttggcctattccatttagt-atttttattgttgttacctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCCATCTCCTGGTCAAGGATTTTCCCTG
     ||| | || | |  | ||  ||     | | | | | |  | | |  |  ||  |  |    |  || | | ||  |||||  |          ||||||||| | ||  |  ||||||   ||||||| |||||||| || ||||| ||||| |||||||||||||||||||
--gagtcaagttaatcaataatgaatttcggcagcttgataattgcttactttttttttctgaaagaagataattacttacattgtcttcttgctagcacagGAAGATGTTGATCTCTTGAAAAGCCTGAATTTCGATGCATATCGGTTTTCAATCTCGTGGTCAAGGATTTTCCCTG

upper sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AC217401.3_FGT001 (Zea mays), 3'ss of exon 2
----------------aatcatcatgatattgagcattggttgatatatcataacagt-----accatt----cactagttggcctattccatttag---tatttttattgttgttacctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCCATCTCCTGGTCAAGGATTTTCCCTG
                 || |  ||| ||  |  |||   |  |  | | ||    ||     ||  ||     |  ||   | || ||  | ||     |  |  | ||||  |      ||| ||||||||| | ||| | ||||||| ||||||||||||||| ||||| ||||| ||||| ||||| ||||| ||||| |
gtactgctccttattatatgacaatgctagagtccatctatctaggttttatgctggtgaaaaacttttgaagtaaaagaaagtctgttagacttgtacttggtccttttgtcatgcaacattttcagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG

upper sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AC217401.3_FGT002 (Zea mays), 3'ss of exon 2
aatcatcatgatattgagcattggttgatatatcataacagtaccattcactagttggc--ctattccatttagtat---ttttattgttgttacctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCCATCTCCTGGTCAAGGATTTTCCCTG
       | || |   | |||     | |      ||| | |  |||| |  | || |   ||||| | |||||| |   |||   |  | |  ||  | | ||||||||| | ||  | |||||||   | ||||||||||||||||| ||||| ||||||||||| ||||| ||||| |
---tgaaacga-acaaaacatctcacgctgagaattaataat-tcatttagaaattagtaactatttcttttagtctgaatttggcttctttatcccttgtacagGAAGATGTTGATCTCATGAAAAGCCTAAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAG

upper sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G148176_T01 (Zea mays), 3'ss of exon 2
aatcatcatgatattgagcattggttga-tatatcataacagtaccattcactagttggcctattccatttagtatt--tttattgttgttacctgtttg-cagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCCATCTCCTGGTCAAGGATTTTCCCTG
               | |  ||   ||| |  ||        |    ||   | | ||  |  |    ||| ||      | |  | ||||    |     ||||||||| || |||||||||| |   ||   |||||||| ||||||||||| ||||| ||||| ||||||||||| |
---------------gtgtgttctctgaatgcattgggttcttcttgttt-ttgggtgctccttgttgtttcgtgacgcctgacggatgttcttcgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG

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|351041108|gb|FQ444085.1|FQ444085
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|352781654|gb|FQ468952.1|FQ468952
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|352778017|gb|FQ467070.1|FQ467070
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|71870097|gb|DT019152.1|DT019152
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAAATTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|349826342|gb|FQ417839.1|FQ417839
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|349826549|gb|FQ418640.1|FQ418640
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|351055499|gb|FQ442295.1|FQ442295
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|352777870|gb|FQ466923.1|FQ466923
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|352763933|gb|FQ465383.1|FQ465383
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|351047302|gb|FQ454913.1|FQ454913
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|351055347|gb|FQ441945.1|FQ441945
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|352769825|gb|FQ468753.1|FQ468753
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|351019898|gb|FQ439715.1|FQ439715
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|77587229|gb|DV222748.1|DV222748
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAAATTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|161712389|gb|FC061694.1|FC061694
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAAATTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|352777639|gb|FQ466692.1|FQ466692
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|352768049|gb|FQ467448.1|FQ467448
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|351056118|gb|FQ453580.1|FQ453580
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|352768397|gb|FQ469573.1|FQ469573
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|351016119|gb|FQ432074.1|FQ432074
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAGGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|351043324|gb|FQ451376.1|FQ451376
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|351016022|gb|FQ431977.1|FQ431977
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|71873314|gb|DT022369.1|DT022369
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAAATTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|351032857|gb|FQ461746.1|FQ461746
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|110425826|gb|EC992219.1|EC992219
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|351044375|gb|FQ452927.1|FQ452927
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|352790248|gb|FQ481447.1|FQ481447
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC
EST: gi|161718844|gb|FC066359.1|FC066359
EST:     CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAG                         GAAGATCTGGACATAATGAAAAATTTGAATTTTGATGCATACCGATTTTCC
genomic: CTGAAAACGGAACCGCTGACGTGGCGGTGGACCAGTACCATCGGTACAAGgtatggtcta ... ctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcactagttggcctattccatttagtatttttattgttgttacctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCCATCTCCTGGTCAAGGATTTTCCCTG
                                            cctgttt  CT-rich tract
                     atttagtatttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcatcatgatattgagcattggttgatatatcataacagtaccattcactagttggcctattccatttagtatttttattgttgttacctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCCATCTCCTGGTCAAGGATTTTCCCTG

- -catcatg
- - - - - - - - - - -tggttga
- - - - - - - - - - - - - - - - -cataaca
- - - - - - - - - - - - - - - - - - - - - -ccattca
- - - - - - - - - - - - - - - - - - - - - - - - - -tagttgg