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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcacatcttgtcttctttgccaggacctgagttctacacgaaaaacatttcatattaaaaataatttctgattcttacatgactattttctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTGTATGAACTGAAGCTGTCGTTGATTGATGAGATTGGATGGGCCCATTTGG

Basic information

species Vitis vinifera
transcript Vv16s0050g00490.t01
intron # 33
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g00490.t01 (Vitis vinifera), 3'ss of exon 33
lower sequence: GLYMA16G30190.1 (Glycine max), 3'ss of exon 33
tctcacatcttgtcttctttgcca--ggacctgagttctacacgaaaaacatttcatattaaaaat--aatttctgattcttacatgactattttctggat-cagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTGTATGAACTGAAGCTGTCGTTGATTGATGAGATTGGATGGGCCCATTTGG
       | |  || ||  ||  |   | | |||  | | |||  |    ||   | || ||  |   || | || | |  |  |   ||  |  || ||| ||||||||    ||||| ||||||||| ||| ||||||| | ||||||||  | ||||| || ||||| || ||| ||||||||||||||||| | |||||||
-----tctttgatcctcagtgagatttgccttgaagtattcactcagcttatagtagataaaccaccaaactacttacttctgaacctcttctcacttgattcagGTACTGTGTGACATAATTCAAGATGACGCAGAGCCTGCCAAGAAGAAATTCTATGACCTTAAGCTCTCTTTGCTTGATGAGATTGGATGGACACATTTGG

upper sequence: Vv16s0050g00490.t01 (Vitis vinifera), 3'ss of exon 33
lower sequence: GLYMA09G25250.1 (Glycine max), 3'ss of exon 33
tctcacatcttgtcttctttgccaggacctgagttctacacgaaaaacatttcatattaaaaata----atttctgattcttacatgactattttctggat-cagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTGTATGAACTGAAGCTGTCGTTGATTGATGAGATTGGATGGGCCCATTTGG
      || ||    | ||    | ||   | | |       |   || ||   ||   |||  |    ||| || | |  |  |   ||| |  || ||| ||||||||    ||||| ||||||||| | |  ||| || | ||||||||| | |||||||| ||||| || ||| ||||||||||||||||| | ||||| |
-----tatatttatattttgatgatgataggtgattggggaaagggactttgggtagataaaccaccaaattacttacttctgaacctctactcccttgattcagGTACTGTGTGACATAATTCAAGATGATGCTGAGGCTGCCAAGAAGAAGTTCTATGAACTAAAGCTCTCTTTGCTTGATGAGATTGGATGGACACATTTAG
















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|349809590|gb|FQ414480.1|FQ414480
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAATAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|349811562|gb|FQ409558.1|FQ409558
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCCGGCTCGGCACAGCACTGAAG                         GTACTAATAGACAT
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACAT
EST: gi|351044162|gb|FQ452835.1|FQ452835
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAATAGACGTGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|110363895|gb|EC927525.1|EC927525
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|110358499|gb|EC922755.1|EC922755
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|110360244|gb|EC923096.1|EC923096
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|34363622|gb|CF405207.1|CF405207
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCCCTGAAG                         GTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|349824505|gb|FQ413172.1|FQ413172
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAATAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|349824556|gb|FQ413223.1|FQ413223
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAATAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAACTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|349814862|gb|FQ410085.1|FQ410085
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAATAGACATGATTCAAGATAACGGACAGCCTCCCAAGAAGAA
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAA
EST: gi|349813697|gb|FQ413931.1|FQ413931
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAATAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|349811081|gb|FQ406069.1|FQ406069
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAATAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|351045622|gb|FQ440807.1|FQ440807
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|349822506|gb|FQ412770.1|FQ412770
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAATAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|349810172|gb|FQ401618.1|FQ401618
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAATAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|349814599|gb|FQ399239.1|FQ399239
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAATAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|349819862|gb|FQ404534.1|FQ404534
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCT
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTA-GTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCT
EST: gi|349807376|gb|FQ401368.1|FQ401368
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAATAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|349814881|gb|FQ410104.1|FQ410104
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACGGCACTGAAG                         GTACTAATAGACATGATTCAAGATAACGGAGAACCTCCAAAGAAGAAACTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|352795665|gb|FQ480253.1|FQ480253
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|349812607|gb|FQ407226.1|FQ407226
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAATAGACATGATTCAAGATAACGGAGAGCCTCCCAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|349815086|gb|FQ410309.1|FQ410309
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAATAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCCG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|351047462|gb|FQ454954.1|FQ454954
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|110359847|gb|EC922069.1|EC922069
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
EST: gi|351053468|gb|FQ459215.1|FQ459215
EST:     TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAG                         GTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG
genomic: TCTGGGTGGTGCGTGAGAGACGCTGTGGCAGGCTCGGCACAGCACTGAAGgtattcttct ... tctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatttcatattaaaaataatttctgattcttacatgactattttctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTGTATGAACTGAAGCTGTCGTTGATTGATGAGATTGGATGGGCCCATTTGG
                            ttcttac  putative branch site (score: 2)
                                       ctattttct  putative PPT
     ttcatattaaaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcacatcttgtcttctttgccaggacctgagttctacacgaaaaacatttcatattaaaaataatttctgattcttacatgactattttctggatcagGTACTAGTAGACATGATTCAAGATAACGGAGAGCCTCCAAAGAAGAAGCTGTATGAACTGAAGCTGTCGTTGATTGATGAGATTGGATGGGCCCATTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
-ctcacat
- - - - - tgtcttc
- - - - - - - - - -tgccagg
- - - - - - - - - - - - - - - - - -ctacacg
- - - - - - - - - - - - - - - - - - - - - aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa