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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatactatatatgtgtgtgtgtgttccctttgtgcactaaaactcttaattttaactcaatactgttttttctgattgattatatgtttgctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGACAAGGCAAAAGACATTTGCCAACATTCTTCACAAAGATCTTAAATTTCC

Basic information

species Vitis vinifera
transcript Vv06s0004g03700.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os11g01140.3 (Oryza sativa), 3'ss of exon 20
-------------------------------------------------------------------------------------------------aaatactatatatgtgtgtgtgtgttccctttgtgcactaaaactcttaattttaactcaatactgtttt----ttctgattgattatatgtttgctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGACAAGGCAAAAGACATTTGCCAACATTCTTCACAAAGATCTTAAATTTCC
                                                                                                 ||||| | || |      |     |  | |   ||   || |   ||  ||   |  |   ||  ||| |    |  || |     || | |||| |  || ||| |||||||||||||||||| | ||||| |||||||| ||||| ||||| || ||||||  ||||||||| || ||  | ||||| ||| | | ||||||
gtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatg-gttacattactgtatcagacatggttatggttatgaggtggtggtaatgaatctatttgttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCC

upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os12g01140.1 (Oryza sativa), 3'ss of exon 20
-------------------------------------------------------------------------------------------------aaatactatatatgtgtgtgtgtgttccctttgtgcactaaaactcttaattttaactcaatactgtttt----ttctgattgattatatgtttgctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGACAAGGCAAAAGACATTTGCCAACATTCTTCACAAAGATCTTAAATTTCC
                                                                                                 ||||| | || |      |     |  | |   ||   || |   ||  ||   |  |   ||  |||      |  || |     || | |||| |  || ||| |||||||||||||||||| | ||||| |||||||| ||||| ||||| || ||||||  ||||||||| || ||  | ||||| ||| | | ||||||
gtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatg-gttacattactgtatcagacatggttatggttacgaggtggtggtaatgaatctatttgttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCC

upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G001457_T01 (Zea mays), 3'ss of exon 1
aaatactatatatgtgtgtgtgtgttccctttgtgcactaaaactcttaattttaactcaa-tactgttt--tttctgattgattatatgtttgctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGACAAGGCAAAAGACATTTGCCAACATTCTTCACAAAGATCTTAAATTTCC
                     ||      | | ||  ||||||     |  | | |  ||  |||| | |  |      ||   | | |  | | | | | ||| |||||||||||||| ||| | ||||| |||||||| || || || || ||||| |||| ||||||||| || ||||| ||||| ||| | | ||||||
---------------------gtaactaatct-tgtgctaaaagaaacatgtatgatacagctactatatgatagtgagttctctttctactggttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAACAAGACAAAGGACATTTGCTAATATTCTGCACAAGGATATCAGATTTCC

upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA15G04850.1 (Glycine max), 3'ss of exon 20
aaatactatatatgtgtgtgtgtgttccctttgtgcactaaaactcttaatt--ttaactcaatactgttttttctgattgattatatgtttg--ctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGACAAGGCAAAAGACATTTGCCAACATTCTTCACAAAGATCTTAAATTTCC
    |    |||||  |||  |  ||   |     ||     | |   |||   ||||    |||     ||   |||  | | |  |   ||   | ||||||| |||||  ||||||||||||||||||| ||||| |||||| |||| |||||||| ||||| |||||||| || ||||||||||| ||||||||||||||
----atatcatatgactgttggacttttttacacacaaagggatttcaaataaattaaaattatatcacattgcttgacagttgacttcaatgactttttttagGTATTCTAATATATGAAATGCTTTATGGGTATACGCCATTTCGGGGGAAGACAAGACAAAAAACATTTGCAAATATTCTTCACAAGGATCTTAAATTTCC

upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA13G40550.1 (Glycine max), 3'ss of exon 19
------aaatactatatatgtgtgtgtgtgttccctttgtgcactaaaactcttaattttaactcaatactgt-tttttctgattgattatatgtttgctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGACAAGGCAAAAGACATTTGCCAACATTCTTCACAAAGATCTTAAATTTCC
       | |  |  | ||        |  ||| ||  |   |  || | |   ||    || | || | | | |     || |||| |  |  |    | ||||||| |||||  ||||||||||||||||||| ||||| |||||  |||| || ||||| ||||| |||||||| || ||||||||||| || |||||||||||
ctgtcggactttttcacatacacaaaaggcttcactcgg---atgaatatttggaac---aaattaaaattatatcacattgcttgacttca-atgactttttttagGTATTCTAATATATGAAATGCTTTATGGGTATACGCCATTCCGGGGGAAAACAAGACAAAAAACATTTGCAAATATTCTTCACAAGGACCTTAAATTTCC

upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 21
------aaatactatatatgtgtgtgtgtgttccctttgtgcactaaaactcttaattttaactcaatactgttttttctgattgattatatgtttgctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGACAAGGCAAAAGACATTTGCCAACATTCTTCACAAAGATCTTAAATTTCC
      ||   |   |  |     | |  ||  | ||     |  || || |     |  | || || |   |  |||  || ||   ||   ||   | ||| ||| |||||| ||||||||||| ||||||| ||||||||||| ||||||||||| |||||||  |||||| | || ||||| ||||| || |||||||||||
gaatttaatggccgaaacttaacctattggtctctttcacataa-aagacacacggataca-ctaaaaaacatacttt--gactg--catgccttacttttttcagGAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGACTAGGCAAAGAACATTTACAAATATTCTCCACAAGGACCTTAAATTTCC

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|30324238|gb|CD007500.1|CD007500
EST:     AATCATAACTGGGGCGGGGCACACTAGTGCAGTGGACTGGTGGGCTCTTG                         GCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGA
genomic: AATCATAACTGGGGCGGGGCACACTAGTGCAGTGGACTGGTGGGCTCTTGgtaatttttt ... gctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGA
EST: gi|110731676|gb|EE106306.1|EE106306
EST:     AATCATAACTGGGGCGGGGCACACTAGTGCAGTGGACTGGTGGGCTCTTG                         GCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGA
genomic: AATCATAACTGGGGCGGGGCACACTAGTGCAGTGGACTGGTGGGCTCTTGgtaatttttt ... gctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGA
EST: gi|30324849|gb|CD008111.1|CD008111
EST:     AATCATAACTGGGGCGGGGCACACTAGTGCAGTGGACTGGTGGGCTCTTG                         GCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGG
genomic: AATCATAACTGGGGCGGGGCACACTAGTGCAGTGGACTGGTGGGCTCTTGgtaatttttt ... gctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGG
EST: gi|30323137|gb|CD006399.1|CD006399
EST:     AATCATAACTGGGGCGGGGCACACTAGTGCAGTGGACTGGTGGGCTCTTG                         GCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGA
genomic: AATCATAACTGGGGCGGGGCACACTAGTGCAGTGGACTGGTGGGCTCTTGgtaatttttt ... gctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGA
EST: gi|351036173|gb|FQ464018.1|FQ464018
EST:     AATCATAACTGGGGCGGGGCACACTAGTGCAGTGGACTGGTGGGCTCTTG                         GCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGA
genomic: AATCATAACTGGGGCGGGGCACACTAGTGCAGTGGACTGGTGGGCTCTTGgtaatttttt ... gctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGA
EST: gi|30251622|gb|CB969355.1|CB969355
EST:     AATCATAACTGGGGCGGGGCACACTAGTGCAGTGGACTGGTGGGCTCTTG                         GCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGA
genomic: AATCATAACTGGGGCGGGGCACACTAGTGCAGTGGACTGGTGGGCTCTTGgtaatttttt ... gctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaattttaactcaatactgttttttctgattgattatatgtttgctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGACAAGGCAAAAGACATTTGCCAACATTCTTCACAAAGATCTTAAATTTCC
                                          tttgctctttt  CT-rich tract
                              attgattatatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatactatatatgtgtgtgtgtgttccctttgtgcactaaaactcttaattttaactcaatactgttttttctgattgattatatgtttgctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGACAAGGCAAAAGACATTTGCCAACATTCTTCACAAAGATCTTAAATTTCC

- - - - - - -gtgtgtg
- - - - - - - - - - - tgttccc
- - - - - - - - - - - - - - -tttgtgc
- - - - - - - - - - - - - - - - - - -ctaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - aactcaa