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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttctatcttctgccattgcataactgaacaaaattttgtgcactaaaagcaactttatttttctaaaatatctattatatgttgaaaacatggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG

Basic information

species Vitis vinifera
transcript Vv16s0022g01690.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0022g01690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os06g04460.1 (Oryza sativa), 3'ss of exon 3
----ctttctatcttctgccattgcataactgaacaaaattttgtgcactaaaagcaactttatttttctaaaatatctattatatgttgaaaacatggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG
    |    | ||    | |  | |||   |       ||  | | | |  |  | |  ||   |  |||   | || |  || ||  |  |  | |    ||||||||||||| ||| || || | ||| |||||||| || |||||||| || || ||||||||| |||||||||  ||||||||||| ||||||||||
gaatcacaatgtccatggtctgttcatctttttcttcgatggtcttctcgtactgtagtttctgtcgtcttgca-atttgataaatcctagatgctt---ccagGTGATGGGAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGACATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAG

upper sequence: Vv16s0022g01690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G026884_T01 (Zea mays), 3'ss of exon 2
ctttctatcttctgccattgcataactgaacaaaattttgtgcactaaa-agcaactttat---ttttctaaaatatctattatatgttgaaaacatggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG
      ||  ||  |  ||  |    |      | |    ||||  | |  ||  || |||   ||| ||   | ||  | || |   |       | |  |||||||||| || ||| || || | ||| |||||||| || ||||||||||| || ||||| ||| |||| || ||||||||||| || ||||||||||
--gagaataatccactgttctaccttttcttgtattgccctgcaacatatggctgctctatgtctttcctggcaaattcaataaactcttgc--tgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAG

upper sequence: Vv16s0022g01690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G32990.1 (Glycine max), 3'ss of exon 3
-ctttctatcttctgccattgcataactgaacaaaattttgtgcactaaaagcaactttattt-ttctaaaatatctattatatgttgaaaacatggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG
  ||  | |  | |    ||  | |  |||  |  |    |    |     ||   || |||| | ||  | ||| |||    ||   |   |||| |||||||||||||||  || |||||||  |||||||||||||| ||||||||||||||||||||| || |||| || ||||||||||||||||| |||||||
tattgttgttgtatttgttttgaaatatgatgatgagcaagattgccttgtgcttgttcatttatgcttgattatttatctcctg--aatttcatgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAG

upper sequence: Vv16s0022g01690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G28170.1 (Glycine max), 3'ss of exon 3
ctttctatcttctgccattgcataactgaacaaaattttgtgcactaaaagcaactttatttttcta-----aaatatctattatatgttgaaaacatggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG
      || | ||    |   |  | ||  |     || || || | |  ||    |||||| |||       ||| |||||      || |   |||| |||||||||||||||  || || ||||  |||||||||||||| ||||||||||||||||||||| || |||| || ||||||||||||||||| ||||| |
---gaaatatactaagttaataagattgtgctgtgctt-gttcatttat-gctctattatttatctgcataccaatgtctatatctccttcatttcatgtatcagGTGATGGGAGAGTATGGCTATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCCG

upper sequence: Vv16s0022g01690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G51570.1 (Arabidopsis thaliana), 3'ss of exon 3
ctttctatcttctgccattgcataactgaacaaaattttgtgcactaaaagcaactttatttttctaaaatatctatta--tatg-ttgaaaacatggat-----cagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG
            |   |    |||   ||    |   |   ||  |  |  |   |  |   || |  |||    || |   ||| ||| |    |   |     ||||||||||| ||||| ||||| | ||| |||||||| || |||||||| ||||| |||||| | |||||||||||||||||||| || || |||||||
-----agaaaagtaataacatatattcgagggtagcct---gctttcgagactggtgaagacttttgtaatggtcatgactcatgattggagttgtttgtttcttcagGTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATTATTCCTGATCCCTCTGTACGCAAGGCAATGAACGAAATCAATGCAG

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|34542871|gb|CF511103.1|CF511103
EST:     GGAGCTTGAGAAG                         GTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATT
genomic: GGAGCTTGAGAAGgtaatttgat ... catggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATT
EST: gi|110393502|gb|EC958789.1|EC958789
EST:     TTGAACAAAAGGGTGATGTTGCTCAAACCGTCTTGGAGGAGCTTGAGAAG                         GTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATT
genomic: TTGAACAAAAGGGTGATGTTGCTCAAACCGTCTTGGAGGAGCTTGAGAAGgtaatttgat ... catggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATT
EST: gi|161716029|gb|FC065535.1|FC065535
EST:     TTGAACAAAAGGGTGATGTTGCTCAAACCGTCTTGGAGGAGCTTGAGAAG                         GTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATT
genomic: TTGAACAAAAGGGTGATGTTGCTCAAACCGTCTTGGAGGAGCTTGAGAAGgtaatttgat ... catggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATT
EST: gi|34542787|gb|CF511019.1|CF511019
EST:     TCTTGGAGGAGCTTGAGAAG                         GTGATGGGAGCTTACGGATAT-AGATCAGAGCACATACTGATGGTTGATAT
genomic: TCTTGGAGGAGCTTGAGAAGgtaatttgat ... catggatcagGTGATGGGAGCTTACGGATATAACAT-AGAGCACATACTGATGGTTGATAT
EST: gi|110366549|gb|EC930459.1|EC930459
EST:     GGAGCTTGAGAAG                         GTGATGGGAGCTTACGGATATAAACATAGAGCACATACTGATGGTTGATAT
genomic: GGAGCTTGAGAAGgtaatttgat ... catggatcagGTGATGGGAGCTTACGGATAT-AACATAGAGCACATACTGATGGTTGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaagcaactttatttttctaaaatatctattatatgttgaaaacatggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG
                 ttctaaa  putative branch site (score: 2)
       aactttatttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttctatcttctgccattgcataactgaacaaaattttgtgcactaaaagcaactttatttttctaaaatatctattatatgttgaaaacatggatcagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAG

- - - - - tctgcca
- - - - - - - - - - - - - - aacaaaa
- - - - - - - - - - - - - - - - - - tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - -aaagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgaaaa