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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgaagtacttcatttggtggtttctctatttttaggtcataggcctttccaggttaggatgctttatgcatggaagtctggcattctctttgatgctttaatctgtctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG

Basic information

species Vitis vinifera
transcript Vv18s0001g02550.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G12110.1 (Glycine max), 3'ss of exon 5
gtaagttgaagtacttcatttggtggtttctctatttttaggtcataggcctttccaggttaggatgctttatgcatggaagtctggcattctctttgatgctttaatctgtctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG
                   |  |||    |   ||||  |      |||   ||  |  ||  | ||| |   | | |  |  |    |  || | | ||       ||  |||||| | |||||||||| || |||||||| |||||||| ||||| || |||||||||||||| || || ||||||||||
------------------gtaagtgaa--catgatttccatagttgaggatattatattttctggtgcatatagaaagttaagccaataacctttctcat-------tcaatctttcttcagGTTATCTATACAGATGTTGCATTAGATCCTTATTCGTCAGATGGGCATGATGGCATAGTTAGAGAAGATG

upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G42670.1 (Glycine max), 3'ss of exon 6
gtaagttgaagtacttcatttggtggtttctctatttttaggtcataggcctttccaggttaggatgctttatgcatggaagtctggcattctctttgatgctttaatctgtctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG
          |||  | |     |  ||||  || |||  ||  ||     ||||  |       ||| | | | | |  |  |    |  || | | ||       ||  |||||| | |||||||||| || |||||||| |||||||| ||||| || |||||||||||||| || || ||||||||||
----------gtaagtgaac--ataatttccatagtttgtggatattatattttctgg-------tgcataaagaaagttaagccaataacctttctcat-------tcaatctttcttcagGTTATCTATACAGATGTTGCATTAGATCCTTATTCATCAGATGGGCATGATGGCATAGTTAGAGAAGATG
















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|352789677|gb|FQ476275.1|FQ476275
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|351023176|gb|FQ432559.1|FQ432559
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|351039238|gb|FQ457913.1|FQ457913
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|349830570|gb|FQ416868.1|FQ416868
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|351036615|gb|FQ457328.1|FQ457328
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|349828957|gb|FQ419290.1|FQ419290
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|351052784|gb|FQ456511.1|FQ456511
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|110386828|gb|EC951456.1|EC951456
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|351044566|gb|FQ443097.1|FQ443097
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|110373793|gb|EC938150.1|EC938150
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|351055179|gb|FQ440518.1|FQ440518
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|351012975|gb|FQ433702.1|FQ433702
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|351020103|gb|FQ445710.1|FQ445710
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCCTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|351054528|gb|FQ452004.1|FQ452004
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAAATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|349830492|gb|FQ416790.1|FQ416790
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|351015476|gb|FQ447305.1|FQ447305
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATGCCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
EST: gi|349826066|gb|FQ415871.1|FQ415871
EST:     GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTT                         GTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT
genomic: GTTTAGTGCCCCGGACAATTCGATTGCTCAAAGACAGATACCCTGATCTTgtaagttgaa ... ctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttatgcatggaagtctggcattctctttgatgctttaatctgtctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG
                                  ctttaat  putative branch site (score: 4)
                                        tctgtctttc  CT-rich tract
                                   tttaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgaagtacttcatttggtggtttctctatttttaggtcataggcctttccaggttaggatgctttatgcatggaagtctggcattctctttgatgctttaatctgtctttcattagGTTATCTACACTGATGTTGCTTTAGATCCGTATTCCTCTGATGGGCATGATGGTATTGTCAGAGAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG