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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGTCCCTGCAAAGTGATGGCTCCAAAATTCCAAGAATTGTCTGGGAAGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAGgtctgtaatcttttacctgatcccaattccctgatacaaatgcacgagctcacactgattcatctgagaactgttggcag

Basic information

species Vitis vinifera
transcript Vv04s0023g00740.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00740.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G017419_T01 (Zea mays), 5'ss of exon 2
GTGTGGTCCCTGCAAAGTGATGGCTCCAAAATTCCAAGAATTGTCTGGGAAGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAGgtctgtaatct--tttacctg------atcccaattccctgatac-aaatgcacgagctcacactgat-tcatctgagaactgttggcag-----------
||| || || ||||||||||||||||| |||||||| ||  |||||| |||| | || || ||||| || || ||||| ||||||||||| |||||||||||  |  | ||    || ||       ||    ||| | |   |      ||| || ||  | ||  | |  | |      |||||               
GTGCGGGCCTTGCAAAGTGATGGCTCCGAAATTCCAGGAGATGTCTGAGAAGAACCTGGATGTTGTGTTCCTGAAGCTCGACTGCAACCAGGACAACAAGgtgaggtagctagcatagctaggatatatagttattactttgcattggccgcatgatctacctcttctcttctttatctgttgttgttgttgttgttgcag

upper sequence: Vv04s0023g00740.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G025954_T01 (Zea mays), 5'ss of exon 2
GTGTGGTCCCTGCAAAGTGATGGCTCCAAAATTCCAAGAATTGTCTGGGAAGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAGgtctgtaatcttttacctgatcccaattccctgatacaaatgcacgagctcacactgattcatctgagaactgttggcag--------------------------------------------------------------------------------
||| || || ||||||||||||||||| || ||||| ||  |||| | |||| | || ||||| || || || ||||||||||||||||| |||||||||||| | || ||   |  |  | |  |  | |   |||  |    | ||||  |   |||| |  |        ||| ||                                                                                 
GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaact---agatagtacgtacgcac--gtacgtacctcctagctagctaggatt-acttagctgtgattgacatatatgatctacgacctagctcgatcttcccttgatctcttctgtgtgcatgcatggcgcttttgcttgttgttcttgcag

upper sequence: Vv04s0023g00740.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA18G47850.1 (Glycine max), 5'ss of exon 2
GTGTGGTCCCTGCAAAGTGATGGCTCCAAAATTCCAAGAATTGTCTGGGAAGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAGgtctgtaatcttttacctgatcccaattccctgatacaaatgcacgagctcacactgattcatctgagaact--gttggcag-----------------------------------
|||||| || |||||||||||||||||||| || |||||||| ||||  |||||||| || ||||||||||||||||| || |||||||||||||||| ||| ||  || |  |     ||   ||||   | ||  | |  |  |      |    | | | |  | |  |   ||| ||                                    
GTGTGGCCCTTGCAAAGTGATGGCTCCAAAGTTTCAAGAATTATCTGAAAAGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatg-gatgtaatgtgctattttaatttatttatgaacacccttgcttaagcctaaagttaaccaatactttccttgacaaacatggtattaatttgtttaatggtttgttggcag

upper sequence: Vv04s0023g00740.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA09G38470.1 (Glycine max), 5'ss of exon 2
GTGTGGTCCCTGCAAAGTGATGGCTCCAAAATTCCAAGAATTGTCTGGGAAGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAGgtctgtaatcttttacctgatcccaattccctgatacaaatgcacg--agctcacact--gattcatctgagaact--gttggcag-----------------------------------
|||||| || |||||||||||||||||||| || |||||||| ||||  |||||||| || ||||||||||||||||| || ||||||||||| |||| ||| || |     | | || |||  ||||   | ||  |  | |||    ||| |  |    | | | |  | |  |  |||| ||                                    
GTGTGGCCCTTGCAAAGTGATGGCTCCAAAGTTTCAAGAATTATCTGAAAAGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGAGAACAGGgtatggatgtaatgagct-atcttaattaatttatttatttacacccttgcttaagcctaaagttaaccaatactttcgttgacaaacatggtattaatttgtttaatggtttgttcgcag

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|30330257|gb|CD013519.1|CD013519
EST:     AGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAG                         ACTTTGGCAAAGGAGCTGGGAATCAGGGTGGTTCCTACCTTCAAGATCCTG
genomic: AGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAGgtctgtaatc ... ctgttggcagACTTTGGCAAAGGAGCTGGGAATCAGGGTGGTTCCTACCTTCAAGATCCTG
EST: gi|110416441|gb|EC982423.1|EC982423
EST:     AGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAG                         ACTTTGGCAAAGGAGCTGGGAATCAGGGTGGTTCCTACCTTCAAGATCCTG
genomic: AGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAGgtctgtaatc ... ctgttggcagACTTTGGCAAAGGAGCTGGGAATCAGGGTGGTTCCTACCTTCAAGATCCTG
EST: gi|30329596|gb|CD012858.1|CD012858
EST:     AGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAG                         ACTTTGGCAAAGGAGCTGGGAATCAGGGTGGTTCCTACCTTCAAGATCCTG
genomic: AGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAGgtctgtaatc ... ctgttggcagACTTTGGCAAAGGAGCTGGGAATCAGGGTGGTTCCTACCTTCAAGATCCTG
EST: gi|110421574|gb|EC987872.1|EC987872
EST:     AGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAG                         ACTTTGGCAAAGGAGCTGGGAATCAGGGTGGTTCCTACCTTCAAGATCCTG
genomic: AGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAGgtctgtaatc ... ctgttggcagACTTTGGCAAAGGAGCTGGGAATCAGGGTGGTTCCTACCTTCAAGATCCTG
EST: gi|30323360|gb|CD006622.1|CD006622
EST:     AGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAG                         ACTTTGGCAAAGGAGCTGGGAATCAGGGTGGTTCCTACCTTCAAGATCCTG
genomic: AGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAGgtctgtaatc ... ctgttggcagACTTTGGCAAAGGAGCTGGGAATCAGGGTGGTTCCTACCTTCAAGATCCTG
EST: gi|110416396|gb|EC982377.1|EC982377
EST:     CTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAG                         ACTTTGGCAAAGGAGCTGGGAATCAGGGTGGTTCCTACCTTCAAGATCCTG
genomic: CTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAGgtctgtaatc ... ctgttggcagACTTTGGCAAAGGAGCTGGGAATCAGGGTGGTTCCTACCTTCAAGATCCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGGTCCCTGCAAAGTGATGGCTCCAAAATTCCAAGAATTGTCTGGGAAGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAGgtctgtaatcttttacctgatcccaattccctgatacaaatgcacgagctcacactgattcatctgagaactgttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA