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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatagcacttttagttgtttatttgttatctttgtgacaaaagtggtttgagggggagggtttgggtggttgatactttctatttcatgttctgcatttgaaaggataaacatatttggtttttctcactaataactaagagttgtgtttatatttcctgctgccagGCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTTTCGTGATTACCAAGTCGATGCAATTACTTTGGAGATTTCACCTAAAGTTGCTTTGAATAATAAGA

Basic information

species Vitis vinifera
transcript Vv14s0066g00580.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G00420.1 (Glycine max), 3'ss of exon 5
gtgcatagcacttttagttgtttatttgttatctttgtgacaaaagtggtttgagggggagggtttgggtggttgatactttctatttcatgttctgcatttgaaaggataaacatatttggtttttctcactaataactaagagttgtgtttatatttcctgctgccagGCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTTTCGTGATTACCAAGTCGATGCAATTACTTTGGAGATTTCACCTAAAGTTGCTTTGAATAATAAGA
                                                                          |    |||||  | |    |||  || ||     |  |  |||||   | |  |    | |||  |     || | | ||||||     ||  ||||  || ||||||||||||||  | |||||||| || |||||||| ||||| |||||||| ||  |||| |||||||| |||||| || | | ||| | ||
--------------------------------------------------------------------------gtgtttttcttctaccccgtctaaatatgttt--actataatattccctgtgaccactttatagttgttctttatctgtatattattc-ctctcagGGCTTAGGTGTTCCCACTGGTCCTCATGGTGCCTTCCGTGATTATCAAGTTGATGCAATCACACTGGAAATTTCACCAAAAGTTTCTCTTACTAAAATGA

upper sequence: Vv14s0066g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G08990.1 (Glycine max), 3'ss of exon 6
gtgcatagcacttttagttgtttatttgttatctttgtgacaaaagtggtttgagggggagggtttgggtggttgatactttctatttcatgttc-tgcatttgaaaggataaacatatttggtttttctcactaataactaagagttgtgtttatat-ttcctgctgccagGCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTTTCGTGATTACCAAGTCGATGCAATTACTTTGGAGATTTCACCTAAAGTTGCTTTGAATAATAAGA
                                                                       ||   |   || ||   ||| |   ||  |||      |||  |   | ||     | |   || ||| ||    || | | | ||| ||  | ||  ||||  || ||||||||||||||  | |||||||| || || ||||| ||||| |||||||| ||  |||| |||||||| |||||| || | | ||| | ||
-----------------------------------------------------------------------gtgtttttcttttaccccatctaaatgtgtttactgtaatattccc-tgtgaccacttttttta-taagtattcttt-tatctgtatattattcctctcagGGCTTAGGTGTTCCCACTGGTCCTCATGGTGCCTTCCGAGATTATCAAGTTGATGCAATCACACTGGAAATTTCACCAAAAGTTTCTCTTACTAAAATGA
















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|349827338|gb|FQ421611.1|FQ421611
EST:     CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCAG                         GCATTGGGTGTTCCCACTGCCTCCCATGGTG
genomic: CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCAGgtgcatagca ... ctgctgccagGCATTGGGTGTTCCCACTGGCTCCCATGGTG
EST: gi|351022494|gb|FQ447016.1|FQ447016
EST:     CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCGG                         GCATTGGGTGTTCC-ACTGGCTCCCA
genomic: CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCAGgtgcatagca ... ctgctgccagGCATTGGGTGTTCCCACTGGCTCCCA
EST: gi|349829802|gb|FQ422115.1|FQ422115
EST:     CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCAG                         GCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTTTCGTGATTACCAA
genomic: CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCAGgtgcatagca ... ctgctgccagGCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTTTCGTGATTACCAA
EST: gi|351018482|gb|FQ439294.1|FQ439294
EST:     AGATTATATGGAAGGAGCTGCCACACTTGGCA-GTTCTTTGTATTACCAG                         GCATTGGGTGTTCCCACGGGCTCCCA
genomic: AGATTATATGGAAGGAGCTGCCACACTTG-CAAGTTCTTTGTATTACCAGgtgcatagca ... ctgctgccagGCATTGGGTGTTCCCACTGGCTCCCA
EST: gi|349825954|gb|FQ415759.1|FQ415759
EST:     CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCGG                         GCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTTTCGTGATTACCAAGTC
genomic: CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCAGgtgcatagca ... ctgctgccagGCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTTTCGTGATTACCAAGTC
EST: gi|351012834|gb|FQ430397.1|FQ430397
EST:     CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCAG                         GCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTTT
genomic: CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCAGgtgcatagca ... ctgctgccagGCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTTT
EST: gi|351015144|gb|FQ444433.1|FQ444433
EST:     CAGATTATATGGAAGGAGCTGCAACACTTGCAAGTTCTTTGTATTACCAG                         GCATTGGGTGTTCCC
genomic: CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCAGgtgcatagca ... ctgctgccagGCATTGGGTGTTCCC
EST: gi|351015113|gb|FQ444402.1|FQ444402
EST:     CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACG-G                         GCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTT
genomic: CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCAGgtgcatagca ... ctgctgccagGCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTT
EST: gi|349830693|gb|FQ416991.1|FQ416991
EST:     CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCAG                         GCATTGGGTGTTCCCACTGGCTCCCATGTTGCTTTTCGTGATTACCAAGTC
genomic: CAGATTATATGGAAGGAGCTGCCACACTTGCAAGTTCTTTGTATTACCAGgtgcatagca ... ctgctgccagGCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTTTCGTGATTACCAAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttggtttttctcactaataactaagagttgtgtttatatttcctgctgccagGCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTTTCGTGATTACCAAGTCGATGCAATTACTTTGGAGATTTCACCTAAAGTTGCTTTGAATAATAAGA
                 taataac  putative branch site (score: 1)
                                         tttcctgct  putative PPT
                              ttgtgtttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatagcacttttagttgtttatttgttatctttgtgacaaaagtggtttgagggggagggtttgggtggttgatactttctatttcatgttctgcatttgaaaggataaacatatttggtttttctcactaataactaagagttgtgtttatatttcctgctgccagGCATTGGGTGTTCCCACTGGCTCCCATGGTGCTTTTCGTGATTACCAAGTCGATGCAATTACTTTGGAGATTTCACCTAAAGTTGCTTTGAATAATAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT