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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacatgaatttgtaattgtgccatatcccttttttctagctgtatgtgttctctatgaacggatatgtttgatgaataatttgctattttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA

Basic information

species Vitis vinifera
transcript Vv06s0004g04800.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g62420.3 (Oryza sativa), 3'ss of exon 5
-ctacatgaatttgtaattgtgccatatcccttttttctagctgtatgtgttctctatgaacggatatgtttgatgaataatttgct-attttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA-----
 ||  |||  |||     |      ||      |    |||  || | | |  | | |  ||   ||  |||  ||  |  ||| ||  |  | | ||||||| ||  | ||    |||   ||| |||||||||| |||||||| |||||||||||||| || || ||||||||||||||||||||||| |||||      
tctttatggcttttgtggtccattgtactgtgctgacatagaagtct-tctcatttctccacccctaactttt-tgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGGTATT

upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
-ctacatgaatttgtaattgtgccatatcccttttttctagctgtatgtgttctctatgaacggatatgtttgatgaataatttgct-attttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA
 ||  |||  |||     |      ||      |    |||  || | | |  | | |  ||   ||  |||  ||  |  ||| ||  |  | | ||||||| ||  | ||    |||   ||| |||||||||| |||||||| |||||||||||||| || || ||||||||||||||||||||||| ||||| 
tctttatggcttttgtggtccattgtactgtgctgacatagaagtct-tctcatttctccacccctaactttt-tgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG

upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 5
ctacatgaatttgtaatt-gtgccatatcccttttttct-agctgtatgtgttctctatgaacggatatgtttgatgaataatttgctattttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA
  |    |  |  |  || |     ||| ||||    |  |  ||   |  ||||  ||      |  |   || | | |   |  |  |||| | || |||||||| | |||   |||   |||||||| ||||| |||||||| |||||||| ||||| || || || |||||||| ||||||||||| ||||| 
-cattctagctgctgctttgaattttattccttcacgcagaaatgagggacttctgaatttctctaattcactgtttactgcctctcc-ttttgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG

upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G41120.1 (Glycine max), 3'ss of exon 5
-ctacatgaatttgtaattgt-gccatatcccttttttctagctgtatgtgttctctatgaacggatatgtttgatgaataatttgctattttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA
  || |  ||  |||  |  | ||  || |   || |  |  |   |  || | | |    |   || | | |  |   | |  |  ||  |    || |||  ||| | ||||  ||||| ||| | |||||||| ||||| || |||||||||||||| || |||||||||||||| ||||||||||| || || 
gttaaaaaaaactgttctaattgctttaacagattatcatctcatcacttgctattttgttagcaatctatattttcgctgacct--taagtgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG

upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G04290.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------------------------ctacatgaatttgtaattg---tgccatatcccttttttctagctgtatgtgttctctatgaacggatatgtttgatgaataatttgctattttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA
                                                                                                    | |  ||||  ||||||   |  || ||     || |||       ||  |  | | | | |  || | | |  |   | |  |  || ||    || |||  ||| | ||||  ||||| ||| | |||||||| || || || |||||||||||||| || ||||||||||| || ||||||||||| || || 
gtaccttttttctccgtatatacaggtttaattttctgcgtattcattaagtcgtgtttttatctcagatttggaggtctttgctgttcttgtttaaaaaaaaaaaattcctaattgctttaacagattatcattatctcatcacttgc-tattttgttagca-atctatattttcgctgacct--taattgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTACGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCTACTCCTGCTCAGGCTCAAGAG

upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G04290.2 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------------------------ctacatgaatttgtaattg---tgccatatcccttttttctagctgtatgtgttctctatgaacggatatgtttgatgaataatttgctattttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA-----
                                                                                                    | |  ||||  ||||||   |  || ||     || |||       ||  |  | | | | |  || | | |  |   | |  |  || ||    || |||  ||| | ||||  ||||| ||| | |||||||| || || || |||||||||||||| || ||||||||||| || ||||||||||| || ||      
gtaccttttttctccgtatatacaggtttaattttctgcgtattcattaagtcgtgtttttatctcagatttggaggtctttgctgttcttgtttaaaaaaaaaaaattcctaattgctttaacagattatcattatctcatcacttgc-tattttgttagca-atctatattttcgctgacct--taattgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTACGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCTACTCCTGCTCAGGCTCAAGAGGTATG

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|110415564|gb|EC981483.1|EC981483
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|351028511|gb|FQ444792.1|FQ444792
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|30129525|gb|CB914864.1|CB914864
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|110389346|gb|EC954175.1|EC954175
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|22015534|gb|BQ800568.1|BQ800568
EST:     ATCAGGATCTACAATGGCTGTTGTTGCTGCACAAA-TAAAGCGATTGCAG                         AAAAAGTTTCAAGCTGGGATAATATTGTTTTGGCTTATGACCCTGTTTGGC
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|34551021|gb|CF519221.1|CF519221
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|33409412|gb|CF215039.1|CF215039
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|294965195|gb|GW837026.1|GW837026
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCGAGCTGGGATACTATTGTCTTGGCTTATGAAC
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAAC
EST: gi|110378426|gb|EC943557.1|EC943557
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|110692722|gb|EE068329.1|EE068329
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|110395870|gb|EC961544.1|EC961544
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|349826936|gb|FQ419027.1|FQ419027
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|110726667|gb|EE102647.1|EE102647
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|71871008|gb|DT020063.1|DT020063
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|110404715|gb|EC970203.1|EC970203
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|161720486|gb|FC070598.1|FC070598
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|161714171|gb|FC062916.1|FC062916
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|110364963|gb|EC928597.1|EC928597
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|110411583|gb|EC977303.1|EC977303
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
EST: gi|33409496|gb|CF215123.1|CF215123
EST:     ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAG                         AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG
genomic: ATCGGGATCTACAATGGCTGTTGTTGCTGCACAAACTAAAGCGATTGCAGgtacatgttt ... tctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttctctatgaacggatatgtttgatgaataatttgctattttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA
                      gtttgat  putative branch site (score: 5)
                                   tttgctattttctctt  putative PPT
                              aataatttgctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacatgaatttgtaattgtgccatatcccttttttctagctgtatgtgttctctatgaacggatatgtttgatgaataatttgctattttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA

ctacatg
- - - - - - - - - -tgccata
- - - - - - - - - - - - - -ccctttt
- - - - - - - - - - - - - - - - - - - - ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgaataa