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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctatctgtcctctcactcactcacacacacagagagtaaatatgtgtttgctgaactttgttgatctttcttacatatgtgttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG

Basic information

species Vitis vinifera
transcript Vv06s0004g00240.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 2
gtatctatctgtcctctcactcactcacacacacagagagtaaatatgtgtttgctgaactttgttgatct-ttcttacatatgtgttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG
|| |||  |  |   ||       |    ||| |   || |  |  ||     |   || | ||    |||  | |||   |  |  |  || |||||||||| ||||||||||| |||||||| || ||||| || || |||||  |  | |||||||||||||| ||||||
gtctctgaccttttcctgttctctttgttcactc---gattttac-tgctcaggtgaaaatctgaaagtctgcttttatcaacctaatt-tttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 7
gtatctatctgtcctctcactcactcacacacacagagagtaaatatgtgtttgctgaactttgttgatct-ttcttacatatgtgttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG
       |||| ||| |  ||     |    | ||           ||     |   || | ||  | ||| || |||   |  |  |  | ||||||||||| ||||||||||| |||||||| || ||||| || || || ||  |  | || ||||||||||| ||||||
------gtctgaccttttcctgttctatttgctcacttgactttactgctcaggtgaaagtctgaagctctgtttttatgaacctaatt-tgcagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCGAAGCTTGCTGGCGGTGTTGCTGTCATTCAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 8
gtatctatctgtcctctcactcactcacacacacagagagtaaatatgtgtttgctgaactttgttgatctttcttacatatgtgttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG
       |   ||     |  || | | |    |  |   |||||  || ||   | |   |  || |   ||        || |||  |  |||| || || ||||| ||||| |||||||| |||||||| |||||||| ||||| ||||| ||||||||||| ||||||
------gtacatctcaaaaaacattgaaatgtcccaa---taaattggttttatgttacggtgattaagtctt--------tgggtttgtgtagGCTGCTGAACAAGACTATGAAAAGGAAAAGCTTAATGAGAGAATTGCTAAATTATCAGGCGGTGTTGCTGTAATTCAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 8
gtatctatctgtcctctcactcactcacacacaca-gagagtaaatatgtgtttgctgaactttgttgat-ctttcttacat--atgtgttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG
          ||    | |   | |    || | | | ||     | |   |||  || |   ||| | | | ||   |     ||  |||  | |||  ||| |||||||| || |||||||| ||||| ||||| |||||||||||  | || ||||| |||||||||||||||
----------gtatagtaaaagagtatagcatatatgggacctcttttactttttgtggatagtgtagttacattgcaatggtaattggtttgtgcagCAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAG

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|110363904|gb|EC927535.1|EC927535
EST:     GAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
genomic: GAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
EST: gi|351022937|gb|FQ428846.1|FQ428846
EST:     CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GCAGCAGAGCAAGAATACGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
genomic: CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
EST: gi|110701933|gb|EE080073.1|EE080073
EST:     CCCAGGAAACAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GGC-GCAGAGCAAGAATATGAGAAAGAAA
genomic: CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagG-CAGCAGAGCAAGAATATGAGAAGGAAA
EST: gi|110419196|gb|EC985406.1|EC985406
EST:     CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
genomic: CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
EST: gi|37188314|gb|CF607663.1|CF607663
EST:     CCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GCAGCAGAGC---AATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
genomic: CCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
EST: gi|351036299|gb|FQ458674.1|FQ458674
EST:     CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
genomic: CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
EST: gi|34550178|gb|CF518396.1|CF518396
EST:     CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
genomic: CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
EST: gi|349807747|gb|FQ402138.1|FQ402138
EST:     CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
genomic: CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
EST: gi|351034062|gb|FQ447979.1|FQ447979
EST:     CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
genomic: CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
EST: gi|30256318|gb|CB972161.1|CB972161
EST:     CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GCAGCAGAGCAAGAATATG
genomic: CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagGCAGCAGAGCAAGAATATG
EST: gi|110362655|gb|EC926202.1|EC926202
EST:     CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
genomic: CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
EST: gi|110362851|gb|EC926408.1|EC926408
EST:     CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
genomic: CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
EST: gi|34549838|gb|CF518070.1|CF518070
EST:     CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
genomic: CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
EST: gi|33401795|gb|CF207422.1|CF207422
EST:     CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAG                         GCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA
genomic: CCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgtatctatct ... gttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaatatgtgtttgctgaactttgttgatctttcttacatatgtgttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG
                                   ttacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctatctgtcctctcactcactcacacacacagagagtaaatatgtgtttgctgaactttgttgatctttcttacatatgtgttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG

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