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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGGGAGATGTTGCTACTTTCCCACTGAAATTGTACAATGAAATTAGAAGAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCAAGCTGTCAAGgtatgcgacttttctttatgcttagttacttttatgaaccatcttagttgatttgtttaatctgctaattgggtgaagttaccaaaaatacattgttctg...

Basic information

species Vitis vinifera
transcript Vv08s0007g03610.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA0169S00210.1 (Glycine max), 5'ss of exon 9
TGTGGGAGATGTTGCTACTTTCCCACTGAAATTGTACAATGAAATTAGAAGAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCAAGCTGTCAAGgtatgcgacttttctttatgcttagttacttttatgaa--------ccatcttagt--tgatttgtttaatct-gctaattgggtgaagtta--ccaaaaatacattgttctg--------------------------------------------------------------------------------------
||| || |||||||||||||||||  ||||||| |||  |||| | ||||||||||||||||| || ||| | || ||||||||||| || ||||| |||||| |   |||  ||  ||   |     | |  |  ||          ||| | |    |   ||     ||| ||||||| |  ||  |      |||  |   || |||||                                                                                      
TGTTGGTGATGTTGCTACTTTCCCTTTGAAATTATACGGTGAATTGAGAAGAGTTGAACATGTTGATCATTCTCGCAAATCAGCTGAACAGGCTGTGAAGgtaagtagcttacctaaatttgtgagctcatgcacaaaatacatatttatcattgccccggcatgccctctctagctaattagtagatatctgcttaaacgtttctttttctggtcctccaaatcaaagtttccagtaaagagccatgcttgcagactgcagtgctgtttctcattctgtgataacttgttttatgtag

upper sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA10G07820.1 (Glycine max), 5'ss of exon 9
TGTGGGAGATGTTGCTACTTTCCCACTGAAATTGTACAATGAAATTAGAAGAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCAAGCTGTCAAGgtatgcgacttttctttat------gcttagttact-tttatgaacc-atcttagt--tgatttgtttaatct-gctaattgggtgaagttaccaaaaatacattgttctg-----------------------------------------------------------------------------------
||| || |||||||||||||||||  ||||||| |||  |||| | ||||||||||||||||| || ||| | || ||||| ||||| || ||||| |||||| |   |||  ||  ||      ||| |   ||  | ||   |   ||| | |    |   || |   ||| |||| |  |  ||  |   |  |||    || || |                                                                                    
TGTTGGTGATGTTGCTACTTTCCCTTTGAAATTATACGGTGAATTGAGAAGAGTTGAACATGTTGATCATTCTCGCAAATCGGCTGAACAGGCTGTGAAGgtaagtagcttacctaaatttgtcagctcatgcacaatatacatatttatcattgccccggcatgctctctctagctattcagtagatatctgcttaaacgttttttttttctggtcctccaaatcgaagtttcaagtaaagagccaatgcttgcagtgctgtttctcattctgtgattacttgttttatgtag

upper sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT5G03630.1 (Arabidopsis thaliana), 5'ss of exon 9
TGTGGGAGATGTTGCTACTTTCCCACTGAAATTGTACAATGAAATTAGAAGAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCAAGCTGTCAAGgtatgcgacttttctttatgcttagt-tacttttatgaaccatcttagttgatttgtttaatctgctaattgggtgaagttaccaaaaatacattgttctg
  | || ||||| || || |||||| ||||| | ||||||||||| ||| | |||||||| || |||||||| || ||||| ||||| ||||| || ||||||    | | |  |   |  | |   |   || |||||  | ||   |  | |  |   |  ||  ||| |  |||   ||  |  | |   | |     
CATTGGTGATGTAGCCACCTTCCCAATGAAACTCTACAATGAAATGAGACGCGTTGAACACGTTGACCATGCTCGCAAATCCGCTGAACAAGCCGTAAAGgta-ataattataatgcttcttcaacctgtcttaatgaaggagctgtataaaatcatcctaattg--aatcgattga---tataatgattttgtag-----

upper sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT3G52880.1 (Arabidopsis thaliana), 5'ss of exon 9
TGTGGGAGATGTTGCTACTTTCCCACTGAAATTGTACAATGAAATTAGAAGAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCAAGCTGTCAAGgtatgcgactttt-ctttatgcttagttacttttatgaaccatcttagttgatttgtttaatctgctaattgggtgaagttaccaaaaatacattgttctg------------------------------------------------------------
||| || || ||||||||||||||  ||||| |||||   ||  | ||||| || || ||||| |||||| |||| |||||||| ||||||||||| ||||||    |   || |  ||||  |  | |    ||      | |    || ||   |   ||     |        ||  |    |      | | || |                                                             
TGTTGGTGACGTTGCTACTTTCCCTTTGAAAATGTACGGAGACGTGAGAAGGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatgcttacaatatggctgat-atcgctacaccaaaaccctattaatccataccataaaaaatgcaacgcaaactcttgaggcctaaatcttatagattaacatacagttgtatatatctgatgaagcgtttatatatgtgatacattgtggcag

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|110373500|gb|EC937742.1|EC937742
EST:     GAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCAAGCTGTCAAG                         GCAATCAAGGCAAGTGAGGAAGGGAAATCAGTTGAGGAGTATGACTACCTT
genomic: GAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCAAGCTGTCAAGgtatgcgact ... gtttatgcagGCAATCAAGGCAAGTGAGGAAGGGAAATCAGTTGAGGAGTATGACTACCTT
EST: gi|33403613|gb|CF209240.1|CF209240
EST:     GAGTTGAACATGTCGACCATGCCCAGAAATCAGCTGAGCAAGCTGTCAAG                         GCAATCAAGGCAAGTGAGGAAGGGAAATCAGTTGAGGGGTATGACTACCTT
genomic: GAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCAAGCTGTCAAGgtatgcgact ... gtttatgcagGCAATCAAGGCAAGTGAGGAAGGGAAATCAGTTGAGGAGTATGACTACCTT
EST: gi|29784398|gb|CB345068.2|CB345068
EST:     GAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCAAGCTGTCAAG                         GCAATCAAGGCAAGTGAGGAAGGGAAATCAGTTGAGGAGTATGACTACCTT
genomic: GAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCAAGCTGTCAAGgtatgcgact ... gtttatgcagGCAATCAAGGCAAGTGAGGAAGGGAAATCAGTTGAGGAGTATGACTACCTT
EST: gi|26264446|gb|CA815509.1|CA815509
EST:     GAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCGAGCTGTCAAG                         GCAATCAAGGCAAGTGAGGAAGGGAAATCAGTTGAGGAGTATGACTACCTT
genomic: GAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCAAGCTGTCAAGgtatgcgact ... gtttatgcagGCAATCAAGGCAAGTGAGGAAGGGAAATCAGTTGAGGAGTATGACTACCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGGGAGATGTTGCTACTTTCCCACTGAAATTGTACAATGAAATTAGAAGAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCAAGCTGTCAAGgtatgcgacttttctttatgcttagttacttttatgaaccatcttagttgatttgtttaatctgctaattgggtgaagttaccaaaaatacattgttctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata