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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattccttttcctccctttatgttttctttctttcaagtatcatttcctaatttcccttttactttgtgttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG

Basic information

species Vitis vinifera
transcript Vv16s0100g00290.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00290.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G51970.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------gtattattccttttcctccctttat-gttttctttctttcaagtatcatttcctaatttcccttttactttgtgttgtttt--agGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG
            | | |||   ||   |   |  || ||  | |  |  |   || ||    |||      |   |   ||| ||||  ||   ||| || |||||||| | ||||||||| |||||||| || || |||||||||||||||||| || | |||
gtaagacaaagatttgatttgattggatatttggattgtcctgtgaccctttggt-tcggaaccttggaaactgatagatttatgttcattcaaagGTCCTCATGATGTGAGAGTTAGGATGAAAGCTGTTGGTATTTGTGGAAGTGATGTTCATTACCTTAAG
















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|71884490|gb|DT033545.1|DT033545
EST:     TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGG                         GCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
genomic: TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGGgtattattcc ... gttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
EST: gi|37188548|gb|CF607897.1|CF607897
EST:     TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGG                         GCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
genomic: TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGGgtattattcc ... gttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
EST: gi|110702722|gb|EE078942.1|EE078942
EST:     TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGG                         GCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
genomic: TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGGgtattattcc ... gttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
EST: gi|71890669|gb|DT039724.1|DT039724
EST:     TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGG                         GCCCTTATGATGTCAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
genomic: TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGGgtattattcc ... gttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
EST: gi|110711540|gb|EE088133.1|EE088133
EST:     TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGG                         GCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
genomic: TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGGgtattattcc ... gttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
EST: gi|110712208|gb|EE089569.1|EE089569
EST:     TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGG                         GCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
genomic: TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGGgtattattcc ... gttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
EST: gi|26257801|gb|CA808864.1|CA808864
EST:     TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGG                         GCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
genomic: TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGGgtattattcc ... gttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
EST: gi|110712986|gb|EE088512.1|EE088512
EST:     TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGG                         GCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
genomic: TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGGgtattattcc ... gttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
EST: gi|37189545|gb|CF608894.1|CF608894
EST:     TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGG                         GCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
genomic: TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGGgtattattcc ... gttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
EST: gi|46917777|gb|CN547106.1|CN547106
EST:     TCAAGATTCAACCCTACATTCTCCCTTCTCTGG                         GCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
genomic: TCAAGATTCAACCCTACATTCTCCCTTCTCTGGgtattattcc ... gttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
EST: gi|110713392|gb|EE089275.1|EE089275
EST:     TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGG                         GCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
genomic: TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGGgtattattcc ... gttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
EST: gi|71884639|gb|DT033694.1|DT033694
EST:     TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGG                         GCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG
genomic: TCTGGGCATCAAGACCCTCAAGATTCAACCCTACATTCTCCCTTCTCTGGgtattattcc ... gttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttctttcaagtatcatttcctaatttcccttttactttgtgttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG
                      tcctaat  putative branch site (score: 2)
                                              ttgtttt  putative PPT
                                  ttttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattattccttttcctccctttatgttttctttctttcaagtatcatttcctaatttcccttttactttgtgttgttttagGCCCCCATGATGTTAAAGTTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG