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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agattgtattaaaaaaccactgaagcagtggctaaaaatacaagaaagataaaattcatccttccattaattggtcatcagctttctttctgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG

Basic information

species Vitis vinifera
transcript Vv12s0059g01930.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 4
agattgtattaaaaaaccactgaagcagtggctaaaaatacaagaaagataaaattcatccttccattaattggtcatcagctttctttc--tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
| |||   |||    | |  |  |  |     |||     | |  | | || |||      |    | |   ||  ||    | ||||    || | || ||||||||||||| |||||||||||| |||||||||
acatttgtttagtttaacctt--actatgaattaacttagccattatgctacaatatcatttgttgtaatcaggaaattgattatcttataatgttctgtagGAACTAAAACGAAGGGAAGATGCTATAGCACGAG

upper sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 4
agattgtattaaaaaaccactgaagcagtggctaaaaatacaagaaagataaaattcatccttccattaattggtcatcagctttctttc--tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
    | || |  || |  ||| | | | |   |        | |  | ||| |||      |    |     ||  ||    | ||||    || | || ||||||||||||| |||||||||||| |||||||||
-ttgtttactttaacattact-atgtattaatttggccattatgctatatataatatcatttggtgtactcaggaaattgattatcttataatgttctgtagGAACTAAAACGAAGGGAAGATGCTATAGCACGAG
















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|110418607|gb|EC984768.1|EC984768
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|77584192|gb|DV221151.1|DV221151
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|27584710|gb|CB007405.1|CB007405
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|349811810|gb|FQ410607.1|FQ410607
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|27586086|gb|CB008781.1|CB008781
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|110385536|gb|EC950069.1|EC950069
EST:     -GAGAGGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: GGAGA-GGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|71884369|gb|DT033424.1|DT033424
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|27584919|gb|CB007614.1|CB007614
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|110376126|gb|EC941168.1|EC941168
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|110357026|gb|EC920280.1|EC920280
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|71870414|gb|DT019469.1|DT019469
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|110699817|gb|EE077160.1|EE077160
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|71870410|gb|DT019465.1|DT019465
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|161710538|gb|FC060684.1|FC060684
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAGCTGGA
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAGCTGGA
EST: gi|110722937|gb|EE099679.1|EE099679
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
EST: gi|110722049|gb|EE097937.1|EE097937
EST:     AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG                         GAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
genomic: AGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAGgtacttcact ... tgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagataaaattcatccttccattaattggtcatcagctttctttctgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG
                   cattaat  putative branch site (score: 3)
                                    ctttctttctgctat  putative PPT
     aaaattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agattgtattaaaaaaccactgaagcagtggctaaaaatacaagaaagataaaattcatccttccattaattggtcatcagctttctttctgctatgcagGAACTAAAACGGAGGGAAGATGCTGTAGCACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - -taaaaaa
- - - - - - - - ccactga
- - - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - caagaaa
- - - - - - - - - - - - - - - - - - - - - - - -gataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcagc