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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcttctctaaaattaactagttgtgcagctacatgagttgcttgatatgtgttttttatgaaaagtgtgatgctaatgggtgattgcaattgcaacagTGATCGTTGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTATTCTGGTCACTCCTCTTGGTGCACTCAGCATTATTATCAG

Basic information

species Vitis vinifera
transcript Vv12s0035g00720.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g00720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G28940.1 (Glycine max), 3'ss of exon 2
cttcttctctaaaattaactagttgtgcagctacatgagttgcttgatatgtgttttttatgaaaagtgtgatgctaat------gggtgattgcaattgcaacagTGATCGTTGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTATTCTGGTCACTCCTCTTGGTGCACTCAGCATTATTATCAG
      | | ||    |  ||    |||      ||||||||| |    | |    |  || |||| |   ||  ||||            |||||||| |||||||||| |||||||| ||||| |||||||| |||||||| ||||| ||||||||  ||||||| ||||||||||| || ||||||||||||||
------cacaaagggcatataaagatgctatgctatgagttgcatatactattaagtggattaaaatttctattataattttctaacacatttgcaatttcaacagTGATTGTTGGGGAGATTGCCAATTTTGCAGCTTATGCATTTGCCCCAGCTATATTGGTCACCCCTCTTGGTGCTCTTAGCATTATTATCAG

upper sequence: Vv12s0035g00720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G00560.1 (Glycine max), 3'ss of exon 2
-----cttcttctctaaaattaactagttgtgcagctacatgagttgcttgatatgtgttttttatgaaaagtgtgatgctaatgggtgattgcaattgcaacagTGATCGTTGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTATTCTGGTCACTCCTCTTGGTGCACTCAGCATTATTATCAG
     |||      || |||| | |  |  || || | | |    |  || |  ||  ||     |   |    |  | ||||    |  |||||||| |||||||||| ||||| || ||||| |||||||| |||||||| ||||| ||||||||  ||||||| ||||||||||| || ||||||||||||||
acaaactttccacatacaatttattgat-atg-agttgcgtataatatttaa-gtggattaaaatttctattcttatttctaacacat--ttgcaatttcaacagTGATTGTTGGAGAGATTGCCAATTTTGCAGCTTATGCATTTGCCCCAGCTATATTGGTCACCCCTCTTGGTGCTCTTAGCATTATTATCAG
















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|161715837|gb|FC067434.1|FC067434
EST:     AGGTTATTCTTACTTATATGAGCCACTTTGGTGGGTGGGCATGATAACAA                         TGATCGTTGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTA
genomic: AGGTTATTCTTACTTATATGAGCCACTTTGGTGGGTGGGCATGATAACAAgtgagtttaa ... attgcaacagTGATCGTTGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTA
EST: gi|161706210|gb|FC054968.1|FC054968
EST:     AGGTTATTCTTACTTATATGAGCCACTTTGGTGGGTGGGCATGATAACAA                         TGATCGTCGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTA
genomic: AGGTTATTCTTACTTATATGAGCCACTTTGGTGGGTGGGCATGATAACAAgtgagtttaa ... attgcaacagTGATCGTTGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTA
EST: gi|161717532|gb|FC066885.1|FC066885
EST:     AGGTTATTCTTACTTATATGAGCCACTTTGGTGGGTGGGCATGATAACAA                         TGATCGTTGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTA
genomic: AGGTTATTCTTACTTATATGAGCCACTTTGGTGGGTGGGCATGATAACAAgtgagtttaa ... attgcaacagTGATCGTTGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTA
EST: gi|110713706|gb|EE089862.1|EE089862
EST:     AGGTTATTCTTACTTATATGAGCCACTTTGGTGGGTGGGCATGATAACAA                         TGATCGTCGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTA
genomic: AGGTTATTCTTACTTATATGAGCCACTTTGGTGGGTGGGCATGATAACAAgtgagtttaa ... attgcaacagTGATCGTTGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTA
EST: gi|33403284|gb|CF208911.1|CF208911
EST:     AGGTTATTCTTACTTATATGAGCCACTTTGGTGGGTGGGCATGATAACAA                         TGATCGGCGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTA
genomic: AGGTTATTCTTACTTATATGAGCCACTTTGGTGGGTGGGCATGATAACAAgtgagtttaa ... attgcaacagTGATCGTTGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatgtgttttttatgaaaagtgtgatgctaatgggtgattgcaattgcaacagTGATCGTTGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTATTCTGGTCACTCCTCTTGGTGCACTCAGCATTATTATCAG
                           tgctaat  putative branch site (score: 2)
      tgttttttatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcttctctaaaattaactagttgtgcagctacatgagttgcttgatatgtgttttttatgaaaagtgtgatgctaatgggtgattgcaattgcaacagTGATCGTTGGGGAAATTGCTAATTTTGCTGCTTATGCGTTTGCACCAGCTATTCTGGTCACTCCTCTTGGTGCACTCAGCATTATTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
cttcttc
- - - - - -aaattaa
- - - - - - - - - - - - -tgcagct
- - - - - - - - - - - - - - - - -catgagt
- - - - - - - - - - - - - - - - - - - - tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgc