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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaagaatttgaaatgaattgaaacttggttttgttgtctgaagaagtggcttatgcttgtcttgtag

Basic information

species Vitis vinifera
transcript Vv14s0030g00700.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0030g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os07g19060.2 (Oryza sativa), 5'ss of exon 2
CCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaagaatttgaaatgaattgaaacttggttttgttgtctgaagaagtggcttatgcttgtcttgtag---------------------------------------------------------------
 || |||||||||||||| || |||||||| ||||||||||| ||||| ||||| ||| | |||||||||||||| |||||  | ||||| || || || || |      |||| | ||||  ||   | |||  |||     | |||| ||   | |  | |||| |||                                                                   
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAATCTGAAGACTAATCATAGGgtaat-----gaatgtaaaattcat---accttattttgcacttgtgaaaaaactgatgttacttgacttccgtatatgcagggcacatttgttcttcaagataaccatttccggtggcttactcgtgtttctgtag

upper sequence: Vv14s0030g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os09g06970.1 (Oryza sativa), 5'ss of exon 2
CCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaagaatttgaaatgaattgaaacttggttttgttgtctgaagaagtggcttatgcttgtcttgtag--------
 || |||||||||||||| || |||||||| ||||||||||| ||||| ||||| ||||| ||||||||||| || |||||  | || || || || || || |      |||||| ||||   | | | |||  |||     | |||   |   | |  | |||| |||            
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaat-----gaatttaaaat---tcgtaccttattttgcgcttgtgacagaactgatgttacttgacttccctatatgcag

upper sequence: Vv14s0030g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os07g19060.1 (Oryza sativa), 5'ss of exon 2
CCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaagaatttgaaatgaattgaaacttggttttgttgtctgaagaagtggcttatgcttgtcttgtag--------
 || |||||||||||||| || |||||||| ||||||||||| ||||| ||||| ||| | |||||||||||||| |||||  | ||||| || || || || |      |||| | ||||  ||   | |||  |||     | |||| ||   | |  | |||| |||            
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAATCTGAAGACTAATCATAGGgtaat-----gaatgtaaaattcat---accttattttgcacttgtgaaaaaactgatgttacttgacttccgtatatgcag

upper sequence: Vv14s0030g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM5G886989_T03 (Zea mays), 5'ss of exon 3
CCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaagaatttgaaatgaattgaaacttggttttgttgtctgaagaagtggctt-atgcttgt-cttgtag
 || |||||||||||||| || |||||||||||||||||||| || || ||||| ||||| ||||||||||| || |||||  | || ||||| ||||| |||| | ||  ||       | | ||    |    | |||||       ||  |  ||| |   |||| |  | ||
TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtga-tgcagaaacacctcct-acttttttccccttcttgttaaacactgacatctcttgactattgtacacgcag

upper sequence: Vv14s0030g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G123807_T01 (Zea mays), 5'ss of exon 3
CCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaagaatttgaaatgaattgaaacttggttttgttgtctgaagaagtggctta--tgcttgt-cttgtag
 || |||||||||||||| || |||||||| ||||||||||| ||||||||||| ||||| |||||||| || || |||||  | || ||||| || || |||| | ||  |||      ||   ||    |   | | |||  |    ||  |  |||   | | | | | || ||
ACGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTCTGGTCAGAGCTGTTCAAGAAACAGATTGACAATCTGAAAACAAATCATAGGgtga-tgcagaaatacttcctgt-ctgtttttccttctcgttaaccactgacatctcttgactacctatacatgcag

upper sequence: Vv14s0030g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA19G42850.1 (Glycine max), 5'ss of exon 2
CCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaagaatttgaaatgaattgaaacttggttttgt-tgtctgaagaagtggcttatgcttgtcttgtag---------------
 ||||| |  |||||||| ||||| |||||||| ||||||||||| || ||||||||||||||||||||||| || |||||||| ||||||||||| || |||||||||    | |||       ||     |   | | | | | |  | |  | | || || ||    ||||                
TCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAACTTGAAGACAAACCATAGGgtgagttcagagctctgatcccttatgggtggtatatatatatatatatatatatagtttttgattaaggtgtatttggttctgttgtag

upper sequence: Vv14s0030g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT3G05000.1 (Arabidopsis thaliana), 5'ss of exon 2
CCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagtt--caagaatttgaaatgaattgaaacttgg--ttttgttgtctgaagaagtggcttatg----cttgtcttgtag
  |||| ||||| ||||||||||||||||||||||||||||| ||||||||||||||| ||||||||||||| || || || ||||||||||| ||| | || || |  |  | |||| |  ||||   | ||      | || |||| ||    | |  |  |||     ||    |  ||
AAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAATTTAAAGACAAATCACCGGgtaagataactgggattttacctgaacaaagaccaaaactcttcttgtgtgtgttattcacagatggaatgtttctcttcag

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|30304539|gb|CB981333.1|CB981333
EST:     GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGA                         GGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
genomic: GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaa ... tgtcttgtagGGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
EST: gi|161709339|gb|FC059668.1|FC059668
EST:     GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGA                         GGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
genomic: GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaa ... tgtcttgtagGGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
EST: gi|26262203|gb|CA813266.1|CA813266
EST:     GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGA                         GGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
genomic: GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaa ... tgtcttgtagGGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
EST: gi|26263640|gb|CA814703.1|CA814703
EST:     GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGA                         GGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
genomic: GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaa ... tgtcttgtagGGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
EST: gi|30136525|gb|CB921863.1|CB921863
EST:     GCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGA                         GGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
genomic: GCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaa ... tgtcttgtagGGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
EST: gi|30132412|gb|CB917751.1|CB917751
EST:     GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGA                         GGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
genomic: GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaa ... tgtcttgtagGGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
EST: gi|28966801|gb|CB345834.1|CB345834
EST:     GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGA                         GGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
genomic: GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaa ... tgtcttgtagGGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
EST: gi|26262474|gb|CA813537.1|CA813537
EST:     GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGA                         GGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
genomic: GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaa ... tgtcttgtagGGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
EST: gi|26262213|gb|CA813276.1|CA813276
EST:     GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGA                         GGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
genomic: GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaa ... tgtcttgtagGGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
EST: gi|110361203|gb|EC924659.1|EC924659
EST:     GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGA                         GGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
genomic: GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaa ... tgtcttgtagGGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
EST: gi|30135317|gb|CB920655.1|CB920655
EST:     GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGA                         GGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
genomic: GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaa ... tgtcttgtagGGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
EST: gi|110380802|gb|EC946095.1|EC946095
EST:     GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGA                         GGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA
genomic: GGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaa ... tgtcttgtagGGCACCTTTGTATTACAAGATAATAAGTTCCGTTGGCTTTCACGCATGTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaagaatttgaaatgaattgaaacttggttttgttgtctgaagaagtggcttatgcttgtcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA