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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaaattagtagaaggaatttgcagtaggagtaggttatttatggttttgtgataattaacaaattttttttgtctgattttcaatgttaattgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG

Basic information

species Vitis vinifera
transcript Vv04s0023g03860.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
ctaaattagtagaaggaatt-tgcagtaggagtaggttatttatggttttgtgataattaacaaattttttttgtctgattttcaatgttaattgagct---agATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG
   || |||| | |  | || | ||  |      |  ||          |  | |   || ||     |  || | |  ||  |||||   |||   ||   ||||||||| || ||||||||||||||  | ||||||||||||||||| || ||| || | ||||||
---aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatc-ttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 4
ctaaattagtagaagga-atttgca-gtaggagtaggttatttatggtttt--gtgataattaacaaattttttttgtctgattttcaatgttaattgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG
   || |||| | |  | || |||  | |      |||    ||  |  |   ||   ||    || ||  || |  | | |   |  |  ||   |  || ||||||||| || ||||||||||||||  | ||||||||||||||||| || ||| || | ||||||
---aactagtggcacaacatgtgcgtgaacccacgggtagcataaagcctcaggttgcaagctgcacatccttatattttcacaatgcacatttcattggc-agATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTATCACTACTGCTCAG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 4
ctaaattagtagaaggaatttgcag--taggagtaggttatttatggtt-ttgtgataattaacaaatt-ttttttgtctgattttcaatgttaattgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG
     || ||  ||   |||    |  |      |   |||      || || |   |||||| |  |  || |||  |   |||| ||| | || ||||  ||| ||||| || || |||||||||||||||||||||||||||||||| |||||  |  | | ||||
----ttttgttaaaaatattcttggcctctacacatactatcaccaattgttctttcaattaagagttagttatttaccattttttgaatttgaaatgagacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCATTACCACCGTTCAG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G36880.1 (Glycine max), 3'ss of exon 5
ctaaattagtagaaggaatttgcagtaggagtaggttatttatggttttgtgataattaacaaattttttttgtctgattttcaatgttaattgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG
  ||||   |        ||  |  |  | | |  |||| |      || | | ||  || |     ||  |   |  ||    || |    |||| |||| |||||||| || |||||||||| ||| |||||||||||||| || || ||  |  ||||||||
acaaatggttgttttagtttctccatttgtgcatattatattgatggttttcacaaccaatagtccgttccttattatttcgtgatttgtgatgagatagACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTATTACCACAGCTCAG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 5
-ctaaattagtagaaggaatttgcag--taggagtaggttatttatggttttgtgataattaacaaattttttttgtctgattttcaatgttaattgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG
   | ||   |        ||  ||   |  || ||   |||| ||| ||||     ||  ||  | | | ||   | | ||||   || |  | |||| |||| |||||||| || |||||||||| ||| |||||||||||||| || || ||  |  ||||||||
gacagatggttgttttagtttctcaacttgtgaatattatattgatgattttc--gcaaccaa-gagtctattccttattatttgtgatttgtaatgagatagACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTATTACCACAGCTCAG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 4
ctaaattagtagaaggaatttgcagtaggagtaggttatt-tatggttttgtgataattaacaaattttttttgtctgatt-ttcaatgttaattga-gctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG
   | |   ||| | |  | | |  |   |  ||    ||  | | | ||  |  || | |  |   |    | | ||||| |  ||  ||  |||  |  ||||||||| || ||||| ||||| ||||| ||||||||||||||||| || ||  |  | | ||||
---actgtatagcaagtgtatacctttataaaagacacttgcaagatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 5
ctaaattagtagaaggaatttgcagtaggagtaggttatttatggttttgtgataattaacaaattttttttgt-ctgattttcaatgtt-----aattgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG
     |||      ||    ||| ||  ||   |  ||    |  ||||   ||| |||  |  ||  | | || || || ||   ||||     |  |  || |||||||||||| ||||| ||||||||||| ||||| ||||| ||||| || ||  || | ||||||
--tgcttaactttcgg--cctgctgtctgatccgtctagacctactttta--atagttatgagtttcgtctggtgcttatgttttgtgtttcatcatatatgccagATCTTCGGGATGACAAACAGTTCTTCATTGACCACCCTGGCGCTGTACCAATTACTACTGCTCAG

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|110376013|gb|EC941052.1|EC941052
EST:     GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG                         ATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
genomic: GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTGgttagatttc ... attgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
EST: gi|110713128|gb|EE088780.1|EE088780
EST:     GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG                         ATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
genomic: GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTGgttagatttc ... attgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
EST: gi|110390015|gb|EC954898.1|EC954898
EST:     GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG                         ATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
genomic: GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTGgttagatttc ... attgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
EST: gi|110396036|gb|EC961711.1|EC961711
EST:     GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG                         ATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
genomic: GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTGgttagatttc ... attgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
EST: gi|87586594|gb|DY474807.1|DY474807
EST:     GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG                         ATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
genomic: GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTGgttagatttc ... attgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
EST: gi|110404309|gb|EC969170.1|EC969170
EST:     GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG                         ATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
genomic: GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTGgttagatttc ... attgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
EST: gi|33410493|gb|CF216120.1|CF216120
EST:     GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG                         ATCTTCGGGAAGACAAGCAGTTCTTCGTAGACCATCCTGGTGCTGTGCCCA
genomic: GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTGgttagatttc ... attgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
EST: gi|110366542|gb|EC930452.1|EC930452
EST:     GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTG                         ATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA
genomic: GAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTTGGCACTAAGCTTGgttagatttc ... attgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtgataattaacaaattttttttgtctgattttcaatgttaattgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG
       ataattaacaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaaattagtagaaggaatttgcagtaggagtaggttatttatggttttgtgataattaacaaattttttttgtctgattttcaatgttaattgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - agaagga
- - - - - - - - - - tgcagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtt