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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attatgttgtagttgatcatgtatgactttctcatgagatttgtttatggattttgaagtaaaatttggtggctaacagaagatgtctcttgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTGAATCCTCAGAACAAAGCGGGTAGGATAACGGTAATCACAAGAATGGGAG

Basic information

species Vitis vinifera
transcript Vv18s0001g06250.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g06250.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G37080.2 (Glycine max), 3'ss of exon 3
attatgttgtagttgatcatgtatgact-ttctcatgagatttgtttatggattttgaagtaaaatttggtggctaacagaagatgtctcttgtgctg-cagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTGAATCCTCAGAACAAAGCGGGTAGGATAACGGTAATCACAAGAATGGGAG
      | |||  |||| |  | | |   |||| | |   ||  |||       |||   | |   |||     | |    |  | | || ||   || ||||| || || |||||||| ||||||||| | ||||| || |||||||| ||||||||||| |||||||| || || || || || ||||| || |||||||
----gttcgtacatgattaattgttatcattcttaagcatttgattttcatgcattggcttta---ttgaattttgatt--atgtttttcatgcattggcagGTAAGTGACAAGATGGATCCAAATGAGCTAGTTAAACTCATTGAGATCTTGAATCCTCAAAACAAAGCAGGAAGAATTACTGTGATCACGAGGATGGGAG
















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|110699818|gb|EE077162.1|EE077162
EST:     GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAG                         GTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
genomic: GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAGgtatctactt ... tgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
EST: gi|352768988|gb|FQ468179.1|FQ468179
EST:     TGTTGAGTTTTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAG                         GTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
genomic: TGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAGgtatctactt ... tgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
EST: gi|110701596|gb|EE079344.1|EE079344
EST:     GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAG                         GTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
genomic: GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAGgtatctactt ... tgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
EST: gi|110685780|gb|EE062798.1|EE062798
EST:     GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAG                         GTGAGGCGATA-GATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTT
genomic: GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAGgtatctactt ... tgtgctgcagGTGAG-CGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTT
EST: gi|33405630|gb|CF211257.1|CF211257
EST:     GCTAATCCCCTGGGCATTAAG                         GTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
genomic: GCTAATCCCCTGGGCATTAAGgtatctactt ... tgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
EST: gi|110414480|gb|EC980313.1|EC980313
EST:     GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAG                         GTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
genomic: GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAGgtatctactt ... tgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
EST: gi|33405540|gb|CF211167.1|CF211167
EST:     GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAG                         GTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
genomic: GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAGgtatctactt ... tgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
EST: gi|110361679|gb|EC925171.1|EC925171
EST:     GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAG                         GTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
genomic: GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAGgtatctactt ... tgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
EST: gi|34544849|gb|CF513081.1|CF513081
EST:     GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAG                         GTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
genomic: GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAGgtatctactt ... tgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
EST: gi|110423681|gb|EC990032.1|EC990032
EST:     GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAG                         GTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
genomic: GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAGgtatctactt ... tgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
EST: gi|110689789|gb|EE066321.1|EE066321
EST:     GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAG                         GTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
genomic: GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAGgtatctactt ... tgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
EST: gi|110368361|gb|EC932335.1|EC932335
EST:     GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAG                         GTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
genomic: GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAGgtatctactt ... tgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
EST: gi|110388773|gb|EC953560.1|EC953560
EST:     GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAG                         GTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG
genomic: GTGCCCATGTTGAGTTCTTAAGAGGAGTTGCTAATCCCCTGGGCATTAAGgtatctactt ... tgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggattttgaagtaaaatttggtggctaacagaagatgtctcttgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTGAATCCTCAGAACAAAGCGGGTAGGATAACGGTAATCACAAGAATGGGAG
                         ggctaac  putative branch site (score: 2)
                                      tgtctctt  putative PPT
     attttgaagtaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attatgttgtagttgatcatgtatgactttctcatgagatttgtttatggattttgaagtaaaatttggtggctaacagaagatgtctcttgtgctgcagGTGAGCGATAAGATGGACCCAAATGAGTTGGTTAAGCTGATTGAGATTTTGAATCCTCAGAACAAAGCGGGTAGGATAACGGTAATCACAAGAATGGGAG

- - - - - - - - tcatgta
- - - - - - - - - - - - - - - - catgaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aagtaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacagaa