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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcag

Basic information

species Vitis vinifera
transcript Vv04s0023g03860.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 5'ss of exon 3
TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttag-atggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcag
|||||||||| |||||||  |||||||||| || || ||||||||| |  |||| ||||| || |||||||||||||||||||| |||||||| |||||||  |||   | |    |||   |    | |||  |    ||  || |        | |   |||    |  | | ||| ||  ||| ||    ||||   |  ||                 
TTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGTTTCAAAGAAGgcaagggactcactt-tcattttctgttaataata----ttgatgtgctctttttttcttctttcgctaaagaagtttgttg-gtcatgtttaatttgagatcgtc----------------

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM5G846811_T01 (Zea mays), 5'ss of exon 3
TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcag
|||||||||| |||||||  |||| ||||| || || ||||||||  |  |||| ||||| || ||||| |||||||||||||| |||||||| |||||||  |||   ||||   |       |     | ||  | | |  |   ||    |    |   |  | |||     || || |   ||     |  ||  | | |                 
TTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGTTTCGAAGAAGgcaaggctctgattcttattttctattatttggctttgtgttttctttagtccagcgtcctctggaaatg----cttgtttttagctcatttaccttacagtct-----------------

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM5G803949_T02 (Zea mays), 5'ss of exon 3
TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttatt---atgtcctgggagattttttaatgtttcggcttcattttcag
|||||||||| |||||||  |||| ||||| || || ||||||||  |  |||| ||||| || ||||| || ||||||||||| |||||||| |||||||  ||    ||||   ||            | | | | | || |  ||       |    | | || |||  | ||||||    ||| ||  | |  | ||    ||||  | |   ||  |||
TTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAAGCCAGCTATGAGAATGTTTCGAAGAAGgcaagacactgat---tc------------ttgtattctatatttggttt-----tgttcactctacatgttactttatttcggtgttctctgggcatctt----gttttagttcatttaccag

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G05160.1 (Glycine max), 5'ss of exon 3
TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggacttga---tggatcaaaat--gaagtgatagcactttttag-tgagtaaaggaatacca------attttagatggcaatttattatgtcctgggagattttttaa---tgtttcggcttcattttcag----------------------------------------
||| || |||||  |||||||||||||||| || || |||||||||||||| || ||||||||||| ||||||||||| |||||||||||||||||||||||      |  |   | |  |||| |   |  |  |||   |  | |  |    || | | | | |      |  ||  |||  ||| |  | | |||      ||| |  |    | | ||   || || || |                                         
TTATAATAGATTACGACCTTTGAGTTATCGTGGTGCTGATGTTTTCATATTAGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTTTCCAAGAAGgtactttttccactatagtccaaagtttaagttcctagtgttgctcaaatttagaatgcacttctacatgttacctttaatgtaaatgtgatgtttccataataattgtaaagaactatatcctatttatattaattaaaaagtgctaataaattgtgtgttattttcattttcag

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G08380.1 (Glycine max), 5'ss of exon 4
TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtg-------aggacttgatg-gatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaa--ttttagatggcaatttattatgtcctgggagattttttaatgtttcgg-------cttcattttcag-----------------------------------------
|||||||||||| |||||||||||||| || || || ||||||||||||||||| ||||||||||| ||||||||||| ||||||||||| || || |||||           | ||  || | ||| | ||   ||  || | | ||   |   |  || |  |  |   || |  |||||   | |  | |        |||  | | || |||           |||||||  |                                          
TTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgtacttcgttgcaatttattgtggtcagagtgttttgggagaattcttatttcttttgagaatcatgaggtttctgtatggcctgtaacgaaggatgtatggatcatgttatattttaagaaaataattcatttatataaaaagtcgatgataaattgcatgtctggtttctttttcag

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA16G23340.1 (Glycine max), 5'ss of exon 3
TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggacttgatggatcaaaa---tgaagtgatagcactttttagtgagtaaaggaa----taccaatt---ttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcag------------------------------------------------
||| || |||||  |||||||||||||||| || || |||||||||||||| || |||||||| || ||||||||||| |||||||||||||||||||||||         |    |  ||    |    |  ||| | |  | |      ||| | |    |||   ||   || ||||  ||| || | | |||      ||| |  |         ||| ||||  |                                                 
TTATAATAGATTACGACCTTTGAGTTATCGTGGTGCCGATGTTTTCATATTAGCTTTCTCTCTGATTAGCAAGGCCAGTTATGAAAATGTTTCCAAGAAGgtacttttcccactatttcaaggtttatgttcctagtattcctcaaatttaaaatgcacttttacaggttacattcgatgtaaatgtaatgtttccataacaattgtaaagaaccatatctt-atttatattaatttaaaagtgttaataaacggtgtatgtgttattttcactttcag

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 4
TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgt-------gaggacttgatg-gatcaaaatgaagtga---tagcactttttagtgagtaaaggaataccaa---ttttagatggcaatttattatgtcctgggagattttttaatgtttcg-------gcttcattttcag-----------------------------------------
||| |||||||| |||||||||||||| || || || |||||||||||| |||| ||||||||||| ||||||||||| ||||||||||| || || |||||       |   | ||  || | ||| | ||   ||    ||   ||| ||| | | |     |||   ||   || |  |||||   | || | |        |||  | | || | |           |||||||  |                                          
TTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATACTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgtacttcgtggcaatttattgtggtcatagtgttttgggtgtatttcttcttatttattttgataattataaggtttctgtatggcctgtaatgaaggatgtatggatcatgttatatgttaagaaaataattcatttataaaaaaagtcgatgataaattgcatgtgtggtttcattttcag

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 5'ss of exon 4
TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcatttt-cag
||| |||||||| |||||||||||||| ||||| || ||||||||||| || ||||||||||| ||||| ||||| || ||||| ||||| |||||||||||  |   ||||   || ||  |    |     ||  ||||  |      | ||||||     |  || |  | | | ||  ||  ||      |||||  || ||   |||| |||| |||
TTATAACAGATTAAGACCTTTGAGTTACCGCGGTGCTGATGTTTTCATCTTAGCATTCTCTCTTATCAGTAAGGCTAGTTATGAGAATGTCTCCAAGAAGgtacgtttttga--aatgaatgt----ttgctacaagttttgat------atgaatac-----tctgaagaaagtcttttg-gttgtga-----tttttgctgctttatcttcgttttgcag

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 5'ss of exon 3
TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcag
 || |||||||| |||||||||||||| || || || |||||||||||  | || ||||||||||| || ||||| || ||||| ||||||||||||||||| ||   ||  |          ||| || | | ||| ||||   | | |  || | |||| ||| ||||    | | || | |    |                                
CTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcag--tttcgtc--------cgaactggtcg-actatttaacaattga--gagttccaaattttgatgct--tcttttcttttacag--------------------------------

upper sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: PP1S257_74V6.1 (Physcomitrella patens), 5'ss of exon 3
TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtga-ggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattt-tagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcag
|||||||||| |  ||||| | |||||  | || || ||||| ||  || ||||||||||||||||||||||||| || ||||||||  | || |||||||| |  | |    |   |        | || |   |   |  ||||  |  || |  || | ||  || || |||||    ||||  ||   |  |||  | | |||| |  |   ||  |||
TTACAACAGACTCCGACCTCTTAGTTACAGGGGTGCCGATGTGTTTTTACTGGCATTCTCTCTCATCAGCAAGGCTAGTTATGAAAACATCTCTAAGAAGgtaatagcccctctcagtttgtccttaatgtttttatcctgaagtggatgcag-acgacgagttgatacattgcaatcctctatgcact---atctttactgacgttttg--tgatttggcag

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:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|110713128|gb|EE088780.1|EE088780
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|110390015|gb|EC954898.1|EC954898
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|110396036|gb|EC961711.1|EC961711
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|87586594|gb|DY474807.1|DY474807
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|110404309|gb|EC969170.1|EC969170
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|33410493|gb|CF216120.1|CF216120
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCGATGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
EST: gi|110366542|gb|EC930452.1|EC930452
EST:     TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAG                         TGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT
genomic: TGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggactt ... tcattttcagTGGATTCCAGAATTGAAGCATTATGCACCTGGTGTTCCGATAGTTCTTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgtgaggacttgatggatcaaaatgaagtgatagcactttttagtgagtaaaggaataccaattttagatggcaatttattatgtcctgggagattttttaatgtttcggcttcattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG