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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGAACAAAGGTTAATTGACCTATTCGAAGGACACCCTTATGATATGTATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttatatgggctcaaaactgattcacccatcttgcattttagctgctaatcaacctatgaacacgcacacatatgaacatttgatgagtaggtagtacattgtgacagagcacatattatgggcctttctgtatcatgaatatataaacacttccacatgttaataattttctttttatgcag

Basic information

species Vitis vinifera
transcript Vv12s0028g00960.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G13700.1 (Glycine max), 5'ss of exon 3
-ATGGGAACAAAGGTTAATTGACCTATTCGAAGGACACCCTTATGATATGTATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttatatgggctcaaaactgattcacccatcttgcattttagctgctaatc--aacctatgaacacgcacacatatgaacatttg-atgagtaggtagtacattgtgacagagcacatattatgggcctttctgtatcatgaatatataaacacttccacatgttaataattttctttttatgcag
  ||||| |||||  ||   ||  | || ||||| |  ||||||||||||||||||||||| || || ||||| ||| |||||||||| |||||| |||||||| |   | | |  |  |||  | | ||    ||    | |||||| | |   ||  |   | ||   |   | | | ||   |||||  || || |   |                                                                                         
GGTGGGAGCAAAGACTATACGATGTTTTTGAAGGCCGGCCTTATGATATGTATGATGCTGCCCTCTCAGATACAGTTTCAAAGTACCCAGTTGATATACAggtagaccaaaa-gcccaaaaacttcactctgaaattgaaccttttagttacctttcctagtttgtgggga---aaataaatcttcatttacatcagaattcaa----------------------------------------------------------------------------------------

upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA08G41890.1 (Glycine max), 5'ss of exon 4
ATGGGAACAAAGGTTAATTGACCTATTCGAAGGACACCCTTATGATATGTATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttatatgggctcaaaactgattcacccatcttgcattttagctgctaatc--aacctatgaacacgcacacatatgaacatttg-atgagtaggtagtacattgtgacagagcacatattatgggcctttctgtatcatgaatatataaacacttccacatgttaataattttctttttatgcag
 ||||| ||||| |||  |||  | |||||||| |  ||||||||||||||||||||||| || || ||||| ||  |||||||||| |||||| |||||||| |   | | |  |  |||   || ||    ||    | || ||| | |   ||  |   | ||   |   | | | ||    ||||  || |  |   |                                                                                         
GTGGGAGCAAAGATTATCTGATGTTTTCGAAGGCCGGCCTTATGATATGTATGATGCTGCCCTCTCAGATACAGTCTCAAAGTACCCAGTTGATATACAGgtagacc-acaagcccgtaaactggactctgaaattgaaccttctagttacctttcctagtttgtgggga---aaataaatccttatttacatcaaaattcaaa---------------------------------------------------------------------------------------

upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G45270.1 (Glycine max), 5'ss of exon 3
ATGGGAACAAAGGTTAATTGACCTATTCGAAGGACACCCTTATGATATGTATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttatatgggctcaaaactgattcacccatcttgcattttagctgctaatcaacctatgaacacgcacacatatgaacatttgatgagt--aggtagtacattgtgacagagcacatattatgggcctttctgtatcatgaatatataaacacttccacatgttaataattttctttttatgcag
 ||||| ||| |  | | |||  | || ||||| |  || |||||||||||||||||||| || ||  |||||||  |||||||||| |||||| | ||||||| |||| || |   |||| || |       ||   | |||  | ||  | |         |||||  |  ||||       |||  |  ||   | |  ||   | |||   |                                                                          
GTGGGAGCAACGACTGAGTGATGTTTTTGAAGGTCGACCCTATGATATGTATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCAGTTGATATTCAGgtac-tttacatag--ccaaatctaag------attgagaattacatcttttta---------gaacaaacttacatgaagttctttagttggttttgatgttaatctctgatcaaaa------------------------------------------------------------------------

upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA14G03500.1 (Glycine max), 5'ss of exon 3
ATGGGAACAAAGGTTAATTGACCTATTCGAAGGACACCCTTATGATATGTATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttatatgggctcaaaactgattcacccatcttgcattttagctgctaatcaacctatgaacacgcacacatatgaacatttgatgagtaggtagtacattgtgacagagcacatattatgggcctttctgtatcatgaatatataaacacttccacatgttaataattttctttttatgcag
 ||||| ||| | || | |||  | || ||||| |  || |||||||||||||||||||| || ||  |||||||  |||||||||| |||||| | ||||||| |||| |||  | |||| || |      || |    |||||||      |  |||||      ||  | | |  |    | |||||    | || || |  ||    | |                                                                          
GTGGGAGCAACGATTGAGTGATGTTTTTGAAGGTCGACCCTATGATATGTATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAGgtac-tttacatg--cccaaatctaagcattacacc----attttag-----gacaaacct-----tacataaaaagttctttagttgattttgatgttgttctctgatcaaaattg-----------------------------------------------------------------------

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|351022225|gb|FQ438810.1|FQ438810
EST:     ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAG                         CCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
genomic: ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttat ... ttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
EST: gi|110712808|gb|EE088180.1|EE088180
EST:     ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAG                         CCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGA-AAAATCAAGA
genomic: ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttat ... ttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
EST: gi|29785566|gb|CB342702.2|CB342702
EST:     ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAG                         CCCTTCAAAGACATGATAGAAGGAATGAGGTTGGACCTGATAAAATCAAGA
genomic: ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttat ... ttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
EST: gi|110716794|gb|EE092085.1|EE092085
EST:     ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAG                         CCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
genomic: ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttat ... ttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
EST: gi|351029870|gb|FQ427710.1|FQ427710
EST:     ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAG                         CCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
genomic: ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttat ... ttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
EST: gi|351027652|gb|FQ446819.1|FQ446819
EST:     TGATGCTGCTCTATCGGATACTGTTGGCAA-GTACCCTGTTGATGTACAG                         CCCTTCAAAGACATGATAGAAAGAATGAGGTTGGACCT
genomic: TGATGCTGCTCTATCGGATACTGTTG-CAAAGTACCCTGTTGATGTACAGgtacatttat ... ttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCT
EST: gi|349828503|gb|FQ417245.1|FQ417245
EST:     ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAG                         CCCCTTCAT-GACATGATAGAAGGAAT
genomic: ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttat ... ttttatgcagCCC-TTCAAAGACATGATAGAAGGAAT
EST: gi|349830020|gb|FQ420280.1|FQ420280
EST:     ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAG                         CCCTTCAAAGA
genomic: ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttat ... ttttatgcagCCCTTCAAAGA
EST: gi|110382672|gb|EC946989.1|EC946989
EST:     ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAG                         CCCTTCAAAGACATGATAGAAGGAATGAGGTTGGACCTGAGAAAATCAAGA
genomic: ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttat ... ttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
EST: gi|28959461|gb|CB339731.1|CB339731
EST:     ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAG                         CCCTTCAAAGACATGATAGAAGGAATGAGGTTGGACCTGAGAAAATCAAGA
genomic: ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttat ... ttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
EST: gi|349822698|gb|FQ412962.1|FQ412962
EST:     ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAG                         CCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
genomic: ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttat ... ttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
EST: gi|349824582|gb|FQ413249.1|FQ413249
EST:     ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAG                         CCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
genomic: ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttat ... ttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA
EST: gi|29785565|gb|CB342700.2|CB342700
EST:     ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAG                         CCCTTCAAAGACATGATAGAAGGAATGAGGAT-GGACCTGAGAAAATCAAG
genomic: ATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttat ... ttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAG-ATTGGACCTGAGAAAATCAAG
EST: gi|28958977|gb|CB339489.1|CB339489
EST:     CCTGTTGATGTACAG                         CCCTTCAAAGACATGATAGAAGGAATGAGGTTGGACCTGAGAAAATCAAGA
genomic: CCTGTTGATGTACAGgtacatttat ... ttttatgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGGAACAAAGGTTAATTGACCTATTCGAAGGACACCCTTATGATATGTATGATGCTGCTCTATCGGATACTGTTGCAAAGTACCCTGTTGATGTACAGgtacatttatatgggctcaaaactgattcacccatcttgcattttagctgctaatcaacctatgaacacgcacacatatgaacatttgatgagtaggtagtacattgtgacagagcacatattatgggcctttctgtatcatgaatatataaacacttccacatgttaataattttctttttatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG