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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagaattacggtggcaaatgggtgaaacccaaccaagtttttgcttctaaaatgatgatcaattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT

Basic information

species Vitis vinifera
transcript Vv16s0098g01580.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 4
-atagaattacggtggcaaatgggtgaaacccaaccaa--gtttttgcttctaaaatgatgatcaattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT
  |  || ||   || ||      |   |   |       || ||   |      ||  ||  |  | |     ||    ||| |  |   |  | ||| |||||||||| ||||| |||||||||||||| ||||||||||| ||||||||||||||| |  | ||||||||||||||||||||| | ||| |||| ||| |
ttttaaacta--atgacatgccttttgtagttagttggtcgtcttgattatctggatagtgcactgt-gattcatatttgactgaactgtctcatctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
-atagaa-ttacggtggcaaatggg---tgaaacccaaccaagtttttgcttctaaaatgatgatcaattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT
  ||||| ||||   | || |   |   | |      | ||  |||   ||   |   ||   ||| |||    | | |||    | | |    | ||  | |||||||||||||||| ||||| |||||||||||||||||||| ||||||||||||||| |  | ||||||||| ||||||||||| | ||| |||| ||| |
tttagaagttacatggacacacttgcttttagtgttgagcacatttc--ctgtgagcttgcatatctatttctgacttgaa---ctgtatcacctcttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 4
atagaattacggtggcaaatgggtgaaacccaaccaagtttttgct--tctaaaatgatgatcaattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT
  |   ||    |     |||  |||      | ||  |||    |   ||   |   | |            |     |  | | |    |  |  | |||||||||| ||||| ||||| |||||||| ||||||||||| ||||||||||||||| |  | ||||||||||||||||||||| | ||| |||| ||| |
--attgttgatatatttcatgcatgatctatcagcacatttcctgtgagcttgcactgtaacttgcctatttatgactgagctgtatcacctcctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 4
------------------------atagaattacggtggcaaatgggtg-aaacccaaccaagtttttgcttctaaaatgatgatcaattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT
                        | |   | | |   |  | |   || |||   ||  |  |  |   | || ||||  |      |   |     |    ||  | |   |    | | |||||||||| |||||||||||||| ||||| |||||||| |||||||||||||| |||||||||||||| || |||||||||||||||||  |||| ||| |
gtgagtacttttatacacatacacacaagctaatgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtctgctattctgtttcccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 4
----------atagaattacggtggcaaatgggtgaaacccaaccaagtttttgcttc-taaaatgatgatc--aattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT
           || |   |      |||  |  |||||   ||  |  | ||   | | ||||||  |  |    ||    | ||     | || ||||     || ||  |||||||||||||||||| ||||| ||||| |||||||| |||||||||||||| |||||||||||||| || |||||||||||||||||  |||| ||| |
gtgagtacttttatacacatacacacaagagaatgaaatgaaattatatattctttccataaaattttctttctgatgctaatgtctgctatttctgtttccccttact--agGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGAAAGCT

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 4
-----------------ata-gaattacggtggcaaatgggtgaaacccaaccaagt-ttttgcttctaaaatgatgatcaattgggaagtagaaaact--tatgttcattttttctg--cagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT
                  || || |     |   ||     |   |   |   || | | ||  |  |   |  |   ||   |  || ||  |    |  |||||    ||   ||   |||||||||| |||||||||||||| ||||| |||||||| |||||||||||||| |||||||||||||| || ||||||||||  |||||  |||| ||| |
gtgagaattttttttttttatgagtcttaataagaagaacttattatgtagaaaaatatattattctttccaccaaattctcctctgatgttaatgcttgctatgtctccttcgccttgccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAGTAGAGCACTTGGCAAGCT

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 4
---------------atagaattacggtggcaaatgggtgaaacccaaccaagtttttgcttctaaaatgatgatcaattgggaagtagaaaacttatgttcattttt----tctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT
               |  || |     |   |||    |   |   |   ||  | ||  |  |   |  |   |   ||  || ||  |    |  | ||  |  ||    |   |||||||||| |||||||||||||| ||||| |||||||| ||||||||||| || ||||||  |||||| || |||||||||| | ||||  |||| ||| |
gtgagaattttttttaatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttccacaaaattttcttctgatgttaatgcttgctatttctccttcaccttaccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAATAAAAAGCATAAAAAGGATATTAGCAAGGACAGCCGAGCACTTGGCAAGCT

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 4
atagaattacggtggcaaatgggtgaaacccaaccaagtttttgcttctaaaatgat-gatcaattgggaagtaga----aaacttatgtt--cattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT
            |  |||     | | |  |||  |  | | |     |  |  ||| | |  | || || || |     || ||| ||||   ||  | |  ||||||||||| ||||| || || |||||||| ||||||||||| || || |||||||||||    ||||||||||||||||||||||  ||| |||| ||| |
-------cgatattccaagctaatcatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtgctaaccttttgttgttatgatctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------------atagaattacggtggcaa----atgggtgaaacccaaccaagtttttgcttctaaaatga-----tgatcaattggga----agtagaaaacttatgtt--cattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT
                                                       | |  ||| |  || |||    ||  |  ||||  |  |||     ||  ||  ||  ||     || |  | || ||     || | || ||| ||||   ||  | |  ||||||||||| ||||| || ||  | ||||| ||||||||||| ||||| |||||||||||    ||||||||||||||||||||||  ||| |||| ||| |
gtaatatacttgtgaccaggaatgaattgttttgaattgcattgtgttcaataacaaatgattgctatgccaatgcaataagctaaacatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtggtaaccttttgttgttatgatctgcgcagGTGAGGACTTTGACCACAGGGTGATGGAGTACTTCATCAAGTTGATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
atagaattacggtggcaaatgggtgaaacccaaccaagtttttgcttctaaaatgatgatcaattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT
                        | |     | |||    ||     |          ||  |     ||    ||||| |  |  |    |   ||||||||||| || ||||||||| | ||||| |||||||||||  | ||||||||||||||    ||||| ||||||||||||||| | ||| |||| ||| |
------------------------gtactttgatcaaagccttctccttt---------tctttcttacagctcgaaactaacatctaccaat---gcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ17607 (Selaginella moellendorffii), 3'ss of exon 4
atagaattacggtggcaaatgggtgaaacccaaccaagtttttgcttctaaaatgatgatcaattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT
                        | |     | |||    ||     |          ||  |     ||    ||||| |  |  |    |   ||||||||||| || ||||||||| | ||||| |||||||||||  | ||||||||||||||    ||||| ||||||||||||||| | ||| |||| ||| |
------------------------gtactttgatcaaagccttctccttt---------tctttcttacagctcgaaactgacatctaccaat---gcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGCAAGCT

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|351040683|gb|FQ438227.1|FQ438227
EST:     CAATGGTGTTTTTGAGGTTCTTGCCACTAATGGAGACACTCATCTGGGAG                         GTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGA
genomic: CAATGGTGTTTTTGAGGTTCTTGCCACTAATGGAGACACTCATCTGGGAGgtaagcattg ... ttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGA
EST: gi|351029703|gb|FQ427543.1|FQ427543
EST:     CAATGGTGTTTTTGAGGTTCTTGCCACTAATGGAGACACTCATCTGGGAG                         GTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGA
genomic: CAATGGTGTTTTTGAGGTTCTTGCCACTAATGGAGACACTCATCTGGGAGgtaagcattg ... ttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaaaatgatgatcaattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT
 ttctaaa  putative branch site (score: 2)
                                     tgttcattttttct  putative PPT
                                  ttatgttcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagaattacggtggcaaatgggtgaaacccaaccaagtttttgcttctaaaatgatgatcaattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - gcaaatg
- - - - - - - - - - - - - - -ccaacca
- - - - - - - - - - - - - - - - - - - - - - - - -aaaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tagaaaa