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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacag

Basic information

species Vitis vinifera
transcript Vv05s0020g03080.t01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM2G059381_T02 (Zea mays), 5'ss of exon 4
-------------GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaag----accatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactg-tatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacag
              |||||||| |||||||| ||||| ||| | ||||| |||||||||||||| ||| | |||||||| || ||||| || || |||||||||||    || || || || | ||   ||||| ||        |  |   |       |  |||||    ||||| || |  ||  ||  | | | ||||| | || | |||| | |                                                                               
TGAAAACCTGCAGAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctgaacgatgtc-ttctcgtgtccagttttt-------cttttgggg-------ttgagttt---gtgactgaagtacctactacctacgtgtcttg-tgctttcatttagat-------------------------------------------------------------------------------

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM2G059381_T03 (Zea mays), 5'ss of exon 5
GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaag----accatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactg-tatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacag
 |||||||| |||||||| ||||| ||| | ||||| |||||||||||||| ||| | |||||||| || ||||| || || |||||||||||    || || || || | ||   ||||| ||        |  |   |       |  |||||    ||||| || |  ||  ||  | | | ||||| | || | |||| | |                                                                               
AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctgaacgatgtc-ttctcgtgtccagttttt-------cttttgggg-------ttgagttt---gtgactgaagtacctactacctacgtgtcttg-tgctttcatttagat-------------------------------------------------------------------------------

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 9
GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatact-tcattacctgtgcatttcttagctttgtattaaaagttgttatatgacag
 | ||| || |||||||||||||| ||| | || || |||||||||||| | ||| |||||||||| ||  |||||||||| |||||||||| ||     |  |||| |      | | |  | ||| |  |  |   | |     | ||||   || ||  ||||    |   || | || ||   ||   |    ||||  |||| | | ||  | |  |   ||| | | | | ||| |  ||||||   ||   | |||                  
AAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAGgtaaaaacgtgcactgttttatattttatccattca-gaacttgtgttc-ttgcagaacacttttccttggctatattg----ttgatttacatttt---ccctaggcgctgtt--tgatctcaccgtttttcttcctatattattaatgcct-taaatttctc--ctggattttag-----------------

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 18
GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacag
|||||| || |||||||||||||||||||| ||||| ||||| || ||    ||||||||||| ||||| || || || |||||||||||| ||    |||||| |  || |    | | |     ||| |  | ||  | |  ||   | || |     ||   |    ||  || || |||   |  | |                                                                                        
GAGAGATGTCATTGATGAAGATGGATGGCTACATACTGGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgtaa-gatagcatcattctaattaa--actataatctatatttaataagaaacatggct---tctgaacttaccacccgttattaaattgatttctgtttaatata---------------------------------------------------------------------------------------

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA20G28200.1 (Glycine max), 5'ss of exon 18
GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttgga----tgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacag
|||||| || ||||||||||| |||||||| ||||| ||||| || ||   |||||||||||| ||||| || || || |||||||||| | ||     ||||| |  || |    |  |  |  | ||||||   |        ||  ||   |    | | | |||||| |     || |||  ||                                                                                                
GAGAGATGTCATTGATGAAGACGGATGGCTACATACTGGAGATATTGGGACATGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgtga-gatagcctcattctaattaaactataatcaat-atttaataggaaacatggcttaacttaccacctgtcattaaattgatttctgtttaatacttta-----------------------------------------------------------------------------------------------

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 5'ss of exon 18
GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgt------aaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacag
|| |||||| ||||||||||||||||||||||| || ||||| |||||| | ||| | || ||||| || ||||| || ||||| ||||      ||| | ||  | ||| || |   | |||  |  || ||  ||| |   ||| |  ||      | || |  | | |   |   || | |||                                                                                                    
GAAAGAGGTGATTGATGAAGATGGATGGCTTCACACTGGAGATATAGGTCTGTGGCTGCCGGGAGGACGTCTAAAAATTATTGACAGgttttccaaaaaatcacttgattgttatcagctgtttcttcactaa--aatcaaatctcttggctcacaaagaataagcctacttcttac-tgatgatacaaa------------------------------------------------------------------------------------------------

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 5'ss of exon 21
GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttctta-gctttgtattaaaagttgttatatgacag
  | ||| |  ||||||||||||||||||| ||||| || ||||| || |  ||||| || || ||||| || || ||||||||||||||    |   |  |   |       || | |  |    ||| ||| |        |  |   |  | |     |  | | ||||      |   |  || ||    || |  | ||   | |     | |   ||  ||| ||||  | || | |||   ||   | || | |     ||| ||  |      
ACGGGAGATTTTTGATGAAGATGGATGGCTACATACTGGCGACATCGGGTGTTGGTTGCCAGGTGGTCGACTCAAAATCATTGATAGgtac--tctggactagcgtcacccttagatgtatgct--attgatatttttcatcattcaacgtctggtagtctagatcagtgtacccagttgagtatgttctactcttctaatgttcgaagatcaatccaactttgaatatttcaggagct-ttcatgagttgtacgttctttccttggttattgcag-----

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|71889597|gb|DT038652.1|DT038652
EST:     GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG                         GAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagacca ... tatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
EST: gi|110414986|gb|EC980854.1|EC980854
EST:     GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG                         GAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagacca ... tatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
EST: gi|46917646|gb|CN546975.1|CN546975
EST:     GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG                         GAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagacca ... tatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
EST: gi|71882993|gb|DT032048.1|DT032048
EST:     GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG                         GAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagacca ... tatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
EST: gi|161720583|gb|FC069911.1|FC069911
EST:     GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG                         GAAGAAGAACATTTTTAATTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagacca ... tatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
EST: gi|46917526|gb|CN546855.1|CN546855
EST:     GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG                         GAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagacca ... tatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
EST: gi|71881187|gb|DT030242.1|DT030242
EST:     GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG                         GAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagacca ... tatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
EST: gi|161720400|gb|FC069849.1|FC069849
EST:     GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG                         GAAAAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagacca ... tatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
EST: gi|71882474|gb|DT031529.1|DT031529
EST:     GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG                         GAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagacca ... tatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA