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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatagtccctcttgcactcatgcctagattattgtttacttgatttttcgtttgttttattttctagaatttcatttgatgtttttggatttctagcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCAATGATGAAGTGAAGAGTCATTTGCAG

Basic information

species Vitis vinifera
transcript Vv03s0063g01060.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g01060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g39640.1 (Oryza sativa), 3'ss of exon 3
--gcatagtccctcttgcactcatgcctag-attattgtttacttgatttttcgtttgttttattttctagaatttcatttgatgtttttggatttcta--gcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCAATGATGAAGTGAAGAGTCATTTGCAG
     | ||| |  |     |    ||||| |  |||||||  || |||||| | ||| |    |     |||  |   || ||||||||  |||  |   |||||||| || || ||||||||||| || || ||| |||||||||||||||| ||||||||||| || || ||  |||||
atttgtggtcacattgttgattgctcctagtaaaattgtttgattaattttttgattggtgcgct-----gaaacttgcttaatgtttttttattgttgatgcagCTGCAACTCCCAAGCAGATTAGGGAGCTGATGAAGGTTGATGGCCTCACTAATGATGAAGTCAAAAGCCACCTGCAG

upper sequence: Vv03s0063g01060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G33130.1 (Glycine max), 3'ss of exon 3
gcatagtccctcttgcactcatgcctagatta--ttgtttacttgatttttcgtttgttttattttctagaatttcatttgatgtttttgg-atttctagcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCAATGATGAAGTGAAGAGTCATTTGCAG
  ||    |    || |    |   | ||      || | |    |||   | |||||||  ||   | |  | | |||  |  | | ||   ||  | ||||| || || |||||||| |||||||| || ||||||||||||||||| || || |||||||||||||| ||||| || 
-tatctgtcaatctgtaagtttatttggaagggcatgataataaaattacacctttgtttggttcatttg--tctaattaaacttctgtgctgttaattgcagCAGCTACACCAAAGCAAATTAGAGAGCTTATGCAGGTTGATGGCCTAACTAACGATGAAGTGAAGAGCCATTTACAA

upper sequence: Vv03s0063g01060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G29490.1 (Glycine max), 3'ss of exon 3
gcatagtccctcttgcactcatgccta--gattattgtttacttgatttttcgtttgttttattttctagaatttcatttgatgtttttgg--atttcta--gcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCAATGATGAAGTGAAGAGTCATTTGCAG
  | ||| |          ||    |    | |  |  | |  |||  | |  |||  || ||  |      | |  ||| |   | ||||  ||||| |  |||||  | || |||||||| ||||| |||||||||  ||| |||||||| |||||||||||||| ||||||||||| || 
--aaagttctctacaagaacagatttgacaagtcataatgatatgacctcttatttagttcatgatt----gtctagtttaaatctcttggtcatttcaattgcagCAACTACTCCAAAGCAAATTAGGGAACTCATGAGGGTAGATGGCCTGACCAATGATGAAGTAAAGAGTCATTTACAA

upper sequence: Vv03s0063g01060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G01260.1 (Glycine max), 3'ss of exon 3
gcatagtccctcttgcactcatgcctagattattgtttacttgatttttcgtttgttttattttctagaatttcatttgatgtttttgg--atttcta--gcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCAATGATGAAGTGAAGAGTCATTTGCAG
    ||| | |     |  ||    |     |     || |    || ||  || |||  ||    |   | | |||| |   |  |||  | ||| |  ||||| || || |||||||| ||||| |||||||||  ||| |||||||| |||||||||||||| ||||||||||| || 
----agttctttacagaaacacagatttggcaagtcataatcatattgtctcttatttggttcataattgtctaatttaaatctcctggttacttcgactgcagCAGCTACTCCAAAGCAAATTAGGGAACTCATGAGGGTAGATGGCCTGACCAATGATGAAGTAAAGAGTCATTTACAA

upper sequence: Vv03s0063g01060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G15320.1 (Glycine max), 3'ss of exon 3
-gcatagtccctcttgcactcatgcctagattattgtttacttg--atttttcgtttgttttattttctagaatttcatttgatgtttttggatttctagcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCAATGATGAAGTGAAGAGTCATTTGCAG
   ||   ||   |     | ||    |      || | |  ||  |   || ||||| || ||||     | |    ||   |||| |    ||  | ||||  || || |||||||| |||||||| || ||||| ||||||||||| || || |||||||||||||| ||||| || 
attatctgccaattcaagtttatttggaagggcatgataatatgttacactttgtttggttcatttgtcgaattaaacttctgtgttct---gttaattgcagTAGCAACACCAAAGCAAATTAGAGAGCTTATGCAAGTTGATGGCCTGACTAACGATGAAGTGAAGAGCCATTTACAA

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|110361584|gb|EC925069.1|EC925069
EST:     GCTGCATCGACGGTTTGTCAATGCCTTGCAGCAACTTGGGGGCTCACAAG                         CTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCA
genomic: GCTGCATCGACGGTTTGTCAATGCCTTGCAGCAACTTGGGGGCTCACAAGgttagaaatc ... tttctagcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCA
EST: gi|83275958|gb|DV939966.1|DV939966
EST:     GCTGCATCGACGGTTTGCCAATGCCTTGCAG---CTTGGGGGCTCACAAG                         CTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCA
genomic: GCTGCATCGACGGTTTGTCAATGCCTTGCAGCAACTTGGGGGCTCACAAGgttagaaatc ... tttctagcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCA
EST: gi|110728806|gb|EE104697.1|EE104697
EST:     GCTGCATCGACGGTTTGTCAATGCCTTGCAGCAACTTGGGGGCTCACAAG                         CTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCA
genomic: GCTGCATCGACGGTTTGTCAATGCCTTGCAGCAACTTGGGGGCTCACAAGgttagaaatc ... tttctagcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCA
EST: gi|30303093|gb|CB979887.1|CB979887
EST:     GCTGCATCGACGGTTTGTCAATGCCTTGCAGCAACTTGGGGGCTCACAAG                         CTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCA
genomic: GCTGCATCGACGGTTTGTCAATGCCTTGCAGCAACTTGGGGGCTCACAAGgttagaaatc ... tttctagcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCA
EST: gi|71878908|gb|DT027963.1|DT027963
EST:     GCTGCATCGACGGTTTGTCAATGCCTTGCAGCAACTTGGGGGCTCACAAG                         CTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCA
genomic: GCTGCATCGACGGTTTGTCAATGCCTTGCAGCAACTTGGGGGCTCACAAGgttagaaatc ... tttctagcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCA
EST: gi|77589426|gb|DV223987.1|DV223987
EST:     GCTGCATCGACGGTTTGTCAATGCCTTGCAGCAACTTGGGGGCTCACAAG                         CTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCA
genomic: GCTGCATCGACGGTTTGTCAATGCCTTGCAGCAACTTGGGGGCTCACAAGgttagaaatc ... tttctagcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcgtttgttttattttctagaatttcatttgatgtttttggatttctagcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCAATGATGAAGTGAAGAGTCATTTGCAG
                             atttgat  putative branch site (score: 5)
                                             tttct  putative PPT
      tttgttttattttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatagtccctcttgcactcatgcctagattattgtttacttgatttttcgtttgttttattttctagaatttcatttgatgtttttggatttctagcagCTGCCACCCCAAAGCAGATTAGAGAACTCATGCAGGTTGATGGCCTCACCAATGATGAAGTGAAGAGTCATTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - -ccctctt
- - - - - - - - - tcatgcc