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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTAGGGTGCTCTTCTGCAGATGGTCGGACTTTATTGGAGTCATCGAAGATTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAGgtaccaaaatcattcaatatgtattaaatgtgaattctttgtctaaatagaaattcatggatcctttttattgtattcctctcacttgaag

Basic information

species Vitis vinifera
transcript Vv09s0002g07530.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G086030_T01 (Zea mays), 5'ss of exon 16
TGTAGGGTGCTCTTCTGCAGATGGTCGGACTTTATTGGAGTCATCGAAGATTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAGgtac-caaaatcattcaatatgtatta---aatgtgaattctttgtctaaatagaaattcatggatcctttttattgtattcct---ctcacttgaag------------------------------
||| |  | ||| |||   |||||||| |  ||| |||| ||||||||||| ||  | |||||||||||  |||| |||||||| | ||||||||||||||| |  |   |||  |  | ||| ||    | | | || |  |  | || |   |  | ||   ||  | |||| || | || |    | | ||                                  
TGTGGTCTACTCATCTATTGATGGTCGAAACTTACTGGAATCATCGAAGATGGCATTGGATAAAGGAAAATTAGATGATGCTGTGAGCTATGGAACAAAGgtgcatatggtcaacctttgtgtcttttttattattaacttctgttttagaattatgtccac--attttgtttagtgaaatcatgtatttatttactaaataagtttgtgtgtttttccttactgaag

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA07G03250.1 (Glycine max), 5'ss of exon 17
TGTAGGGTGCTCTTCTGCAGATGGTCGGACTTTATTGGAGTCATCGAAGATTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAGgtaccaaaatcattcaatatgtattaaatg-tgaattctttgt-------ctaaatagaaattcatggatcctttttattgtattcctctcac-ttgaag
|||||||||||| ||   |||||| || | |||||||||||| || || ||||| ||||||||||||||||| ||||||||||| || |||||||||||||||| ||   | |||   |     |  ||| || ||  ||| |       |||  || ||||   |||  |  | || |   | | || |||  | | ||
TGTAGGGTGCTCCTCATTAGATGGACGCAATTTATTGGAGTCTTCCAAAATTGCTCTTGATAAAGGAAAGCTTGAGGATGCTGTGAATTATGGAACAAAGgtacaaatcactttcttcagtctctggatggtgcatcatttctaagtttactagttataaat--gtggcacagtgttttgacaatactatcatatcgcag

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA08G22850.1 (Glycine max), 5'ss of exon 15
TGTAGGGTGCTCTTCTGCAGATGGTCGGACTTTATTGGAGTCATCGAAGATTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAGgtaccaaaatcattcaatatgtattaaatgtgaattctttgtctaaa--tagaaatt-----catggatcctttttattgtattcctctcac-ttgaag
||| |||||||| ||   |||||| || | |||||||||||| || || ||||| ||||||||||||||||| ||||||||||| |  |||||||||||||||| ||   | |||| ||     || ||| |       |||||||   ||  | ||       |||  |  | || |   | |  | |||  ||| ||
TGTTGGGTGCTCCTCAATAGATGGACGCAATTTATTGGAGTCTTCCAAAATTGCTCTTGATAAAGGAAAGCTTGAGGATGCTGTGACTTATGGAACAAAGgtacaaattactttcattagtctctacatg-gtgcatcatgtctaagtttactagttataaatgtggcacagtgttttgacaataatatcatattgcag

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: AT1G15290.1 (Arabidopsis thaliana), 5'ss of exon 14
TGTAGGGTGCTCTTCTGCAGATGGTCGGACTTTATTGGAGTCATCGAAGATTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAGgtaccaaaatcattcaatatgtattaaatgtgaattct--ttgtctaaatagaaattcatg-gatcctt-tttattgtattcctctcacttgaag
|||   |||   |||  | || ||  ||||  | ||||||||||| ||  |||| ||||| |||||||| ||||| |||||||| | |||||||||||||||  ||   || ||  |||  ||    ||    |||||      || ||| |  ||  | | ||| ||   || ||| ||| |            
TGTGCTGTGTATTTCATCTGACGGAAGGACACTCTTGGAGTCATCAAAACTTGCTCTTGACAAAGGAAAACTAGATGATGCTGTGAGCTATGGAACAAAGgtgtcatt-tcttttgatagctacatgatcatcattctaaccaactgaattgttatctaagagatgctgacttcttgcatttcctag--------

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|30326937|gb|CD010199.1|CD010199
EST:     TTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAG                         GCACTGGCAAAGATGATAGCTGTATGTGGTCCATATCATCGAACCACTGCA
genomic: TTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAGgtaccaaaat ... tcacttgaagGCACTGGCAAAGATGATAGCTGTATGTGGTCCATATCATCGAACCACTGCA
EST: gi|32272114|gb|CD721273.1|CD721273
EST:     TTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAG                         GCACTGGCAAAGATGATAGCTGTATGTGGTCCATATCATCGAACCACTGCA
genomic: TTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAGgtaccaaaat ... tcacttgaagGCACTGGCAAAGATGATAGCTGTATGTGGTCCATATCATCGAACCACTGCA
EST: gi|32248906|gb|CD714725.1|CD714725
EST:     TTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAG                         GCACTGGCAAAGATGATAGCTGTATGTGGTCCATATCATCGAACCACTGCA
genomic: TTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAGgtaccaaaat ... tcacttgaagGCACTGGCAAAGATGATAGCTGTATGTGGTCCATATCATCGAACCACTGCA
EST: gi|32249415|gb|CD715234.1|CD715234
EST:     TTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAG                         GCACTGGCAAAGATGATAGCTGTATGTGGTCCATATCATCGAACCACTGCA
genomic: TTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAGgtaccaaaat ... tcacttgaagGCACTGGCAAAGATGATAGCTGTATGTGGTCCATATCATCGAACCACTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTAGGGTGCTCTTCTGCAGATGGTCGGACTTTATTGGAGTCATCGAAGATTGCGCTTGATAAAGGAAAGCTAGAGGATGCTGTTAACTATGGAACAAAGgtaccaaaatcattcaatatgtattaaatgtgaattctttgtctaaatagaaattcatggatcctttttattgtattcctctcacttgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT