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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttgtaatggctgtctgtaatgataatgaatggtagtaacaatagacctaaaccatgttaattttgtcaattaaaactctttggttctcattctgcagAACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCATTCCGGTTGTCATGCTTCCACAAGATGCTGGTGCCAGCTTGGAAAAAAG

Basic information

species Vitis vinifera
transcript Vv15s0046g02460.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G46760.1 (Glycine max), 3'ss of exon 3
--ttgttgtaatggct-gtctgtaatgataatgaatggtagtaacaatagacctaaaccatgttaattttgtcaattaaaactctttggttctcattctgcagAACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCATTCCGGTTGTCATGCTTCCACAAGATGCTGGTGCCAGCTTGGAAAAAAG
  |   | |  |  ||  | |||  | | ||| ||      |      | ||   |   || ||  || | | ||  ||   |  |  |  || ||| ||||||||||||||| |||||||||||||| |||||||||| | |  ||||  | || || | ||||||||||||||||||||||||||  | |||| ||||   
attaactttggtttcttatttgttgttagaataaacatacattttccaatactgca--tattttgtttgttttaagcaactattgtatgcccttattatgcaGAACTTTTCAAGATGGTTTGTGAAGCGAATGAAACTGATGTTGATATTGGAATACCTGCTGTCATGCTTCCACAAGATGCTGGTGAAAACTTGAAAAATC-

upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 3
----ttgttgtaatggct-gtctgtaatgataatgaatggtagtaacaatagacctaaaccatgttaattttgtcaattaaaactctttggttctcattctgcagAACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCATTCCGGTTGTCATGCTTCCACAAGATGCTGGTGCCAGCTTGGAAAAAAG
    |   | |  |  || || ||| || ||||  |    | ||  |||||   ||     || ||  || | | ||  ||   | ||| || ||  || ||||||||||||||| |||||||||||||| |||||||| | | |  ||||  | || || | ||||||||||||||||||||||||||  | |||| ||||   
taattaactttggtttcttgtttgttataataaacagacattgtc-caata---ctgcgt-attttgtttgttttaagcaactattttttgtcctttttatgcagAACTTTTCAAGATGGTTTGTGAAGCAAATGAAACCGATGTTGATATTGGAATACCTGCTGTCATGCTTCCACAAGATGCTGGTGAAAACTTGAAAAATCA

upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G01100.2 (Glycine max), 3'ss of exon 3
ttgttgtaatggctgtctgtaatgataatgaatggtagtaaca-atagacctaaaccatgttaattttgtcaattaaaactctttggttc-tcattctgcagAACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCATTCCGGTTGTCATGCTTCCACAAGATGCTGGTGCCAGCTTGGAAAAAAG
 |      |   ||| |   |||   |   |||  |  |   | ||| |    ||  || |||   |  |     |||    | |  ||| ||  | | ||||||||||||| |||||||||||||  |||||||||| | |  ||||  | || || | ||||||||||||||||||||||||    | ||||||||    
-tacaaagaaaactg-caacaattgaagcaaatatttcttttatataaaatataaaaatattacagtgttttgagaaactaatgtatttcatcgctatacagAACTTTTCAAGATGGTTTGTGAAGAAAATGAAACTGATGTTGATATTGGAATACCTGCTGTCATGCTTCCACAAGATGCTGGATTGACCTTGGAAAGGCA

upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G07610.1 (Glycine max), 3'ss of exon 3
-------ttgttgtaatggctgtctgtaatgataatgaatggtagtaacaatagacctaaaccatgttaattttgtcaattaaaactctttggttctcattctgcagAACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCATTCCGGTTGTCATGCTTCCACAAGATGCTGGTGCCAGCTTGGAAAAAAG
         |||| | |   | | | |  |     |  ||  || ||| ||||    || ||  | ||  |||||  ||   ||  | ||| |||   ||    ||||||||||||| |||||||||||||  |||||||||| | |  ||||  | || || | ||||||||||||||||||||||||    | ||||||||    
cgacaagcagttgaagtaaatatttcttttatatttatataata-taaaaata---ttacactgtatttgttttgagaaagtaatgtatttcgttgctat---acagAACTTTTCAAGATGGTTTGTGAAGAAAATGAAACTGATGTTGATATTGGAATACCTGCTGTCATGCTTCCACAAGATGCTGGATTGAACTTGGAAAGGCA

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|33405906|gb|CF211533.1|CF211533
EST:     TGCAGAAAATGCTGGTGCTTCTGCAGTTCTCATTGTAAACAACCAGACAG                         AACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCA
genomic: TGCAGAAAATGCTGGTGCTTCTGCAGTTCTCATTGTAAACAACCAGACAGgtatgtaggt ... cattctgcagAACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCA
EST: gi|161707763|gb|FC056428.1|FC056428
EST:     TGCAGAAAATGCTGGTGCTTCTGCAGTTCTCATTGTAAACAACCAGACAG                         AACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCA
genomic: TGCAGAAAATGCTGGTGCTTCTGCAGTTCTCATTGTAAACAACCAGACAGgtatgtaggt ... cattctgcagAACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCA
EST: gi|294965942|gb|GW839281.1|GW839281
EST:     TGCAGAAAATGCTGGTGCTTCTGCAGTTCTCATTGTAAACAACCAGACAG                         ACCTTTTCAAAATGGTTTGTGAAGCTAATGAGACTGCTATACATATAAGCA
genomic: TGCAGAAAATGCTGGTGCTTCTGCAGTTCTCATTGTAAACAACCAGACAGgtatgtaggt ... cattctgcagAACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCA
EST: gi|110712809|gb|EE088181.1|EE088181
EST:     TGCAGAAAATGCTGGTGCTTCTGCAGTTCTCATTGTAAACAACCAGACAG                         AACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCA
genomic: TGCAGAAAATGCTGGTGCTTCTGCAGTTCTCATTGTAAACAACCAGACAGgtatgtaggt ... cattctgcagAACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCA
EST: gi|161714434|gb|FC064433.1|FC064433
EST:     TGCAGAAAATGCTGGTGCTTCTGCAGTTCTCATTGTAAACAACCAGACAG                         AACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCA
genomic: TGCAGAAAATGCTGGTGCTTCTGCAGTTCTCATTGTAAACAACCAGACAGgtatgtaggt ... cattctgcagAACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacctaaaccatgttaattttgtcaattaaaactctttggttctcattctgcagAACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCATTCCGGTTGTCATGCTTCCACAAGATGCTGGTGCCAGCTTGGAAAAAAG
            tgttaat  putative branch site (score: 3)
                                         ttctcattct  putative PPT
           atgttaattttgtcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttgtaatggctgtctgtaatgataatgaatggtagtaacaatagacctaaaccatgttaattttgtcaattaaaactctttggttctcattctgcagAACTTTTCAAAATGGTTTGTGAAGCTAATGAAACTGCTATAAATATAAGCATTCCGGTTGTCATGCTTCCACAAGATGCTGGTGCCAGCTTGGAAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - -tgtctgt
- - - - - - - - - - aatgataa
- - - - - - - - - - - - - - tgaatgg
- - - - - - - - - - - - - - - - - - -gtaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - -aaaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aattaaa