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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttttctttcatttgaattctgggttttactgcatatgatgtcaagagctcttattccctgaatggatcgacttaaatgttgccaatacagagaaattttgattgtctagagaaactttacaattttattttattttttaaatttgatcttgcaaatttgaattgatgtgtgtattgggggatctatttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCTTTCATTGCTTGGGAGTTGGAATTCCCTTTAATCACAGTGAAGAAAGCTT

Basic information

species Vitis vinifera
transcript Vv16s0050g01450.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01450.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G29590.1 (Glycine max), 3'ss of exon 3
gtaagcttttctttcatttgaattctgggttttactgcatatgatgtcaagagctcttattccctgaatggatcgacttaaatgttgccaatacagagaaattttgattgtctagagaaactttacaattttattttattttttaaatttgatcttgcaaatttgaattgatgtgtgtattgggggatctatttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCTTTCATTGCTTGGGAGTTGGAATTCCCTTTAATCACAGTGAAGAAAGCTT
||||| ||||| | ||||  | | |    | |    |    |||  | ||      |||  |    | |   | |  ||   | | |  | |   | || ||| | |||   |  ||||||||| |    | |||||  || ||   |    | |||||  | |  |   | ||   | ||      |||   | |  |||| |||| | | |||||||||||||||||||||||||| ||||||||||| |   |||||||||| || || ||||||||||| |||||||| || ||| 
gtaagtttttcct-cattgcattccc---tctagtcgttcctgacattaa-----tttaagcttcaatt---ttgttttctctctgggaagtt--gtgacattctcatttaattcagaaacttt-cggactgatttt--ttcttgggt---gttttgcatttctaga--aaagtaatttttctaatgtct---tctacagATTAAGGAGCTGTCAAATGTCAAAGAGGAAGTTTATGGAGCTCTTGATTCCTATGTTGCTTGGGAATTAGAGTTCCCTTTAATTACAGTGAAAAAGGCTC

upper sequence: Vv16s0050g01450.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G24100.1 (Glycine max), 3'ss of exon 3
gtaagcttttctttcatttgaattctgggttttactgcatatgatgtcaagagctcttattccctgaatggatcgacttaaatgttgccaatacagagaaattttgattgtctagagaaactttacaat-tttattttattttttaaatttgatcttgcaaatttgaattgatgtgtgtattgggggatctatttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCTTTCATTGCTTGGGAGTTGGAATTCCCTTTAATCACAGTGAAGAAAGCTT
                         || ||||| |   ||   |   |         || ||  | | |  | |  | |   ||||  |  | | | ||| || |||   |||     || |    ||  || |   || |||||   || ||| || || ||||      | ||   | ||      |||   | |  |||| ||||   | || ||||||||||||||||||||||| ||||||||||| |   |||||||||| || || ||||||||||| |||||||| || ||  
------------------------gtgagtttttccttattgcactccgg------ctagtcattaatttaagcttcatttttgttttctct-ctgggaagttgtgacactctcatttaattcagaaacattcagactaattttttc-ttggatgtttcacatttatggaaaagtaatttttctaatgtct---tgtacagATTAAGGAACTGTCTAATGTCAAAGAGGAAGTTTATGGAGCTCTTGATTCCTATGTTGCTTGGGAATTAGAGTTCCCTTTAATTACAGTGAAAAAGGCAC

upper sequence: Vv16s0050g01450.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G21190.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagcttttctttcatttgaattctgggttttactgcatatgatgtcaagagctcttattccctgaatggatcgacttaaatgttgccaatacagagaaattttgattgtctagagaaactttacaattttattttattttttaaatttgatcttgcaaatttgaattgatgtgtgtattgggggatctattta---tgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCTTTCATTGCTTGGGAGTTGGAATTCCCTTTAATCACAGTGAAGAAAGCTT
                                                                                                                                     |  |  | | |  || || | |||     |  |||   | |  |  || | |  | |  |||   || ||||||| || || || ||||| ||||| ||||||||||| || |||||||| |||||||||||||| || || |||||| |  | | ||| ||||| || |
------------------------------------------------------------------------------------------------------------------------------------gtaatgctctcttcatatgtttttgtgttctgcaatctcttttagagttagtgagtattgttaatctgcagATAAAAGGATTGTCGAATGTTAAAGAAGAAGTTTATGGAGCGCTTGATTCCTTCATTGCTTGGGAATTAGAGTTCCCTCTTGTTATAGTTAAGAAGGCAT

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|351046546|gb|FQ453162.1|FQ453162
EST:     CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGT                         ATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
genomic: CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGTgtaagctttt ... atttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
EST: gi|351054436|gb|FQ450519.1|FQ450519
EST:     CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGT                         ATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
genomic: CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGTgtaagctttt ... atttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
EST: gi|351033744|gb|FQ462274.1|FQ462274
EST:     CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGT                         ATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
genomic: CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGTgtaagctttt ... atttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
EST: gi|349822100|gb|FQ408429.1|FQ408429
EST:     CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGT                         ATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
genomic: CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGTgtaagctttt ... atttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
EST: gi|349814396|gb|FQ398836.1|FQ398836
EST:     CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGT                         ATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
genomic: CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGTgtaagctttt ... atttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
EST: gi|349815708|gb|FQ400864.1|FQ400864
EST:     CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGT                         ATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
genomic: CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGTgtaagctttt ... atttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
EST: gi|351055367|gb|FQ441965.1|FQ441965
EST:     CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGT                         ATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
genomic: CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGTgtaagctttt ... atttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
EST: gi|22014552|gb|BQ799586.1|BQ799586
EST:     CCAGACAAAGAA-TGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGT                         ATAAAGGGGTTATCAAATGTCAAAGAGGAAG-TTAT-GGGCTCTTGATTCT
genomic: CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGTgtaagctttt ... atttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
EST: gi|349827078|gb|FQ421351.1|FQ421351
EST:     CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGT                         ATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
genomic: CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGTgtaagctttt ... atttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
EST: gi|294965603|gb|GW837202.1|GW837202
EST:     CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGT                         ATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
genomic: CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGTgtaagctttt ... atttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
EST: gi|351052433|gb|FQ452466.1|FQ452466
EST:     CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGT                         ATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
genomic: CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGTgtaagctttt ... atttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
EST: gi|352781628|gb|FQ468926.1|FQ468926
EST:     CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGT                         ATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT
genomic: CCAGACAAAGAATTGGGACCATCTCCAAATCGGCAAAGCTTGTGGATTGTgtaagctttt ... atttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgatcttgcaaatttgaattgatgtgtgtattgggggatctatttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCTTTCATTGCTTGGGAGTTGGAATTCCCTTTAATCACAGTGAAGAAAGCTT
                    aattgat  putative branch site (score: 4)
                                          tctattt  putative PPT
             aaatttgaattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttttctttcatttgaattctgggttttactgcatatgatgtcaagagctcttattccctgaatggatcgacttaaatgttgccaatacagagaaattttgattgtctagagaaactttacaattttattttattttttaaatttgatcttgcaaatttgaattgatgtgtgtattgggggatctatttatgtagATAAAGGGGTTATCAAATGTCAAAGAGGAAGTTTATGGGGCTCTTGATTCTTTCATTGCTTGGGAGTTGGAATTCCCTTTAATCACAGTGAAGAAAGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA