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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccctgacttgatgtttttactatttgtggttgtctagttggtcctgtatttgattaccaaagggaaaaatgatacttatgcgatactattttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCCCTGCGTATTGCTGGTGGAACAATCAAG

Basic information

species Vitis vinifera
transcript Vv08s0105g00460.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g06600.1 (Oryza sativa), 3'ss of exon 3
-tcccctgacttgatgtttttactatttgtggttgtctagttggtcctgtatttgattacc---aaagggaaaaatgatacttatgcgatactattttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCCCTGCGTATTGCTGGTGGAACAATCAAG
 |    | ||| |||  | |  |  ||          |  |||||| | || |    | ||   | | |   | || |   ||  |  |   |  |   | |||||||||||||| |||||||| ||||||||||   |||| || ||| |   |||  || | ||||| || ||||| |||
tttgattaactagataatat-gcccttgacaa--actttattggtcatataataacctgcctttagaagatgacataaccatttcgtaaatttgctac-tgcagTACTGGGAGAAAGCAGAGTTCCCATTTCATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAG

upper sequence: Vv08s0105g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G862219_T02 (Zea mays), 3'ss of exon 3
-tcccctgacttgatgtttttactatttgtggttgtctagttggtcctgtatttg--attaccaaagggaaaaatgatacttatgcgatactattttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCCCTGCGTATTGCTGGTGGAACAATCAAG
 |    | |     ||  |||||    |   ||  |  |    || |   ||      ||   | |    |  || ||  ||||  ||| |  |  ||  ||||||||||| |||||||||||||||||| |||   |||| || |||||   |||  || |||||||||| ||||| |||
tttttattatagtttggatttacgtcctaatgtccttaaagcagttcctcatcaaccttttttatacaatagcataatcattat-tgatgcgctactg--cagTACTGGGAAAAGGCAGAGTTTCCATTTAATGCCATTCCTAAACTTGCAAGCCTTGGTGTTGCTGGTGGTACAATAAAG

upper sequence: Vv08s0105g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G43240.1 (Glycine max), 3'ss of exon 3
tcccctgacttgatgtttttactatttgtggttgtc--tagttggtcctgtatttgattaccaaagggaaaaatgatacttatgcgatactattttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCCCTGCGTATTGCTGGTGGAACAATCAAG
       | || |      | || | |||  || |   |||  |  |      | ||| |    |     | ||||  || ||   | ||| ||||  |||||||||||||||||| || || |||||||||||| | |||||| ||||||||||||||||||||||||| ||||| |||
-aattgaaattaaacagcattctttgtgtatttattattagaggagcaaactgtagataattgtactttcagatgac-ctaatctcacactttttttatcagTACTGGGAGAAGGCTGAATTCCCATTTCATGTTATCCCAAAGTTTGCTGCCCTGCGTATTGCTGGTGGCACAATTAAG

upper sequence: Vv08s0105g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G18370.1 (Glycine max), 3'ss of exon 3
--tcccctgacttgatgtttttactatttgtggttgtctagttggtcctgtatttgattaccaaagggaaaaatgatactta-tgcgatactattttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCCCTGCGTATTGCTGGTGGAACAATCAAG
  | |   |  ||  |    | | || | | ||  |  ||  |  |  | ||||| ||||              || ||| | |   ||| |||||| | ||||||||||||||||| || || |||||||||||| | |||||| ||||||||||||||||||||||||| ||||| |||
tttgctacggttttttagggtgagtagtggagg--ggttaccttttattttattttattatttttaattctcccgacactcaatctcataatattttat-cagTACTGGGAGAAGGCTGAATTCCCATTTCATGTTATCCCAAAGTTTGCTGCCCTGCGTATTGCTGGTGGCACAATTAAG

upper sequence: Vv08s0105g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G07540.1 (Glycine max), 3'ss of exon 3
----------------------tcccctgacttgatgtttttactatttgtggttgtctagttggtcctgtatttgattaccaaagggaaaaatgatacttatgcgatactattttgtt---cagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCCCTGCGTATTGCTGGTGGAACAATCAAG
                         | ||  | ||     |||| || ||   || |             ||| |  || |        ||    ||  | |||| ||  | ||||  |   |||||||||||||||||  ||||||||||||||||| |||||||||||| |||  |||| ||||||||||| |||||||||
gcatgtatttgtgatgctgttactacttggatggaaacaattacgatgtgaaattattctcccataatgttatcttttttctttctttcaatcccatcatcatgcaattttttttttcttctcagTACTGGGAGAAGGCCAAGTTTCCATTTCATGTTATTCCAAAGCTTGGTGCGTTGCGCATTGCTGGTGGCACAATCAAG

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|110378244|gb|EC943364.1|EC943364
EST:     TGAAAGTGAGAAAGTGTGTGGAAAAGGAAATTGCTCCGATAATGACAGAG                         TACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
genomic: TGAAAGTGAGAAAGTGCGTGGAAAAGGAAATTGCTCCGATAATGACAGAGgtattctcct ... ttttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
EST: gi|351030433|gb|FQ432371.1|FQ432371
EST:     TGAAAGTGAGAAAGTGTGTGGAAAAGGAAATTGCTCCGATAATGACAGAG                         TACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
genomic: TGAAAGTGAGAAAGTGCGTGGAAAAGGAAATTGCTCCGATAATGACAGAGgtattctcct ... ttttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
EST: gi|110698070|gb|EE075664.1|EE075664
EST:     TGAAAGTGAGAAAGTGTGTGGAAAAGGAAATTGCTCCGATAATGACAGAG                         TACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
genomic: TGAAAGTGAGAAAGTGCGTGGAAAAGGAAATTGCTCCGATAATGACAGAGgtattctcct ... ttttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
EST: gi|351040358|gb|FQ434491.1|FQ434491
EST:     TGAAAGTGAGAAAGTGTGTGGAAAAGGAAATTGCTCCGATAATGACAGAG                         TACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
genomic: TGAAAGTGAGAAAGTGCGTGGAAAAGGAAATTGCTCCGATAATGACAGAGgtattctcct ... ttttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
EST: gi|349827568|gb|FQ422436.1|FQ422436
EST:     TGAAAGTGAGAAAGTGCGTGGAAAAGGAAATTGCTCCGATAATGACAGAG                         TACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
genomic: TGAAAGTGAGAAAGTGCGTGGAAAAGGAAATTGCTCCGATAATGACAGAGgtattctcct ... ttttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
EST: gi|351023906|gb|FQ423329.1|FQ423329
EST:     TGAAAGTGAGAAAGTGTGTGGAAAAGGAAATTGCTCCGATAATGACAGAG                         TACTGGGAGAAGGCAGAATTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
genomic: TGAAAGTGAGAAAGTGCGTGGAAAAGGAAATTGCTCCGATAATGACAGAGgtattctcct ... ttttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
EST: gi|351041348|gb|FQ447475.1|FQ447475
EST:     TGAAAGTGAGAAAGTGCGTGGAAAAGGAAATTGCTCCGATAATGACAGAG                         TACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
genomic: TGAAAGTGAGAAAGTGCGTGGAAAAGGAAATTGCTCCGATAATGACAGAGgtattctcct ... ttttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
EST: gi|18458097|gb|BM436375.1|BM436375
EST:     TGAAAGTGAGAAAGTGCGTGGAAAAGGAAATTGCTCCGATAATGACAGAG                         TACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
genomic: TGAAAGTGAGAAAGTGCGTGGAAAAGGAAATTGCTCCGATAATGACAGAGgtattctcct ... ttttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
EST: gi|161705479|gb|FC055321.1|FC055321
EST:     TGAAAGTGAGAGAGTGCGTGGAAAAGGAAATTGCTCCGATAATGACAGAG                         TACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC
genomic: TGAAAGTGAGAAAGTGCGTGGAAAAGGAAATTGCTCCGATAATGACAGAGgtattctcct ... ttttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtatttgattaccaaagggaaaaatgatacttatgcgatactattttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCCCTGCGTATTGCTGGTGGAACAATCAAG
    atttgat  putative branch site (score: 5)
                                             ttttgttc  putative PPT
                     aaaaatgatacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcccctgacttgatgtttttactatttgtggttgtctagttggtcctgtatttgattaccaaagggaaaaatgatacttatgcgatactattttgttcagTACTGGGAGAAGGCAGAGTTTCCATTTCATGTTGTTCCAAAGCTTGCTGCCCTGCGTATTGCTGGTGGAACAATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- ccctgac
- - - - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - - tagttgg
- - - - - - - - - - - - - - - - - - - - - -tcctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - taccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttatgc