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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatccgtttgtttccaaggaaaatttccctagaagatttatttccaacaaagtcagtgatttctgattgtattttgtggttgtttgtattgtcctctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGC

Basic information

species Vitis vinifera
transcript Vv08s0105g00280.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 1
gttagtatccgtttgtttccaaggaaaatttccctagaagatttatttccaacaaa-gtcagtgatttctgattgtattttgtggttgtttgtattgtcctctgttt-----cagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGC
||| |    | |  | ||| |      ||| |  | |   |    | |  ||||   ||   || ||| |  ||   || |   ||||||  | | ||     || |      |||||||||| ||||||||||| |  || || |    | ||||||| || |  || || |||||||| ||||||||||||||||| ||| ||||||||||||
gttcgc--tcttcagcttcgatttcgcattcctttggtttaaccttcttaaacatttgttcttgtttttttctttggttcttatgttgttgttgtcgtgtgtcgtgtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGTAAGCGCAAGAAAGAGGCACGTCAAGTTCACAAGC

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G10000.1 (Glycine max), 3'ss of exon 1
gttagtatccgtttg-tttccaaggaaaatttccctagaagatttatttccaacaaagtcagtgatttctgattgtattttgtggttgtttgtattgtcctctg-tttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGC
          ||| | | | |||     ||||| |   |   |||   | |||||   | |    ||| |  |||  | || || |  | | |  |||  | |  || ||||||||||| ||||||||||| | ||| || |    | ||||||| || | ||| || |||||||| ||||||||||||||||| ||| |||||||||| |
----------gttcgctcttcaacttcgatttcgc---actcttttggttcaacattcttaacattttttttttggttcttatgttgttgtcttctgttgtgtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTTGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 1
gttagtatccgtttgtttccaaggaaaatttccctagaagatttatttccaacaaagtcagtgat-ttctgattgtattt-tgtggttgtt-tgtattgtcctctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGC
||| |    | |    ||| |      | | |  | |   |  |  ||   |     ||  |  | || | ||| |  || ||| |||||  ||| ||||      || ||||||||||| ||||||||||| | ||| || |    | ||||||| || |  || || |||||||| ||||||||||||||||| ||| |||||||||| |
gttcgc--tcttcaacttcgatttcgcactcctttggtcaaccttcttgacatttgttcttttttattattattattcttatgttgttgtcgtgtgttgtgta--attgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC

upper sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------gttagtatccgtttgtttccaaggaaaatttc-cctagaagatttatttccaacaaagtcagtgatttctgattgtattttgtggttgtttgtattgtcctctgttt--cagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGC
                   |||| |  ||| ||        |  ||||   |   |||| ||    |   |  ||   |||| ||| |   | || |||||||  || |||||     ||     ||||| || ||||||||||||||  | || |||||| |  |||| |||||||  ||||| |||||| | ||||||||||| ||||| ||||||||||||||||
gtacgttctccgccgccggagtaccttttttttcttcttacagctttcgtttctcagatataacagcttgagcgttt-tgatctctaacaat-ttctgtggtttcttctattggtggatgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGC

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|351034903|gb|FQ458260.1|FQ458260
EST:     AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|37189315|gb|CF608664.1|CF608664
EST:     AAAAACCTGGCGTTTTCTCCAAAACTGTTTCAACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAAAACCT-GCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|351034907|gb|FQ458264.1|FQ458264
EST:     AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|161706371|gb|FC055477.1|FC055477
EST:     AAAACTGTTTCAACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|110689931|gb|EE066589.1|EE066589
EST:     CGTTTTCTCCAAAACTGTTTCAACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: CGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|349827619|gb|FQ422487.1|FQ422487
EST:     AAAACCTGCGTTTTCTCCAAAACTGTTTCAACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAAACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|351012282|gb|FQ429967.1|FQ429967
EST:     AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|351053282|gb|FQ459150.1|FQ459150
EST:     AAAACTGTTTCGACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTACCGCCCT
genomic: AAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|351025564|gb|FQ426380.1|FQ426380
EST:     AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|71875347|gb|DT024402.1|DT024402
EST:     AAAAACCTGCGTTTTCTCC-AAACTGTTTCAACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAAAACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|110686904|gb|EE063847.1|EE063847
EST:     CGTTTTCTCCAAAACTGTTTCAACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: CGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|351035636|gb|FQ463481.1|FQ463481
EST:     AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|349827505|gb|FQ422373.1|FQ422373
EST:     AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|351056948|gb|FQ443575.1|FQ443575
EST:     AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|351032431|gb|FQ458796.1|FQ458796
EST:     AACCTGCGTTTTCTCCAAAACTGTTTCAACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|351049548|gb|FQ429170.1|FQ429170
EST:     AAAACCTGCGTTTTCTCCAAAACTGTTTCAACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAAACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|349830525|gb|FQ416835.1|FQ416835
EST:     AAAACCTGCGTTTTCTCCAAAACTGTTTCGACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAAACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|77588634|gb|DV223535.1|DV223535
EST:     CAAAACTGTTTCAACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: CAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|351049014|gb|FQ431558.1|FQ431558
EST:     AACCTGCGTTTTCTCCAAAACTGTTTCAACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|351056833|gb|FQ443460.1|FQ443460
EST:     AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAACCTGCGTTTTCTCCAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|71875464|gb|DT024519.1|DT024519
EST:     CAAAACTGTTTCAACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: CAAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
EST: gi|161720669|gb|FC070613.1|FC070613
EST:     AAAACTGTTTCAACCATG                         CCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT
genomic: AAAACTGTTTCGACCATGgttagtatcc ... tctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtcagtgatttctgattgtattttgtggttgtttgtattgtcctctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGC
           ttctgat  putative branch site (score: 3)
                                       ttgtcctctgtttc  putative PPT
                attgtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtatccgtttgtttccaaggaaaatttccctagaagatttatttccaacaaagtcagtgatttctgattgtattttgtggttgtttgtattgtcctctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG