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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGTCAACCCCCGGAGAATTGGACTAGTGGAGTAGATCTTGGACGTCTTCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAGgtttgtagttttgaatcgccaaatcgtctttagcatttatttttggtagcctgtttatgtttgattacctttaaatggagaggcaggcttattacccagc...

Basic information

species Vitis vinifera
transcript Vv01s0011g01870.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g01870.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G033724_T02 (Zea mays), 5'ss of exon 5
GTTGGTCAACCCCCGGAGAATTGGACTAGTGGAGTAGATCTTGGACGTCTTCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAGgtttgtagttttgaat-cgccaaatcgtctttagc--atttatttttggtagcctgtttatgtttgattacctttaaatggagaggcaggcttattacccagc-----------------------------------------
  ||  ||   |||  | |||||||| |||||||| |||||||| || ||||| || |  || |||||||||||||||| ||||||||||   ||  |||||| |   || |   | |    | |  | | |     | |  ||||||    ||| || |  |      |  |  |    ||    |     | || |                                              
TGTGACCATGGCCCTCAAAATTGGACCAGTGGAGTTGATCTTGGCCGCCTTCTGGATCGTCTTGAACTTGATCTTATCATAACCAGCGAATCACTCAAAGgttcggcattctccttgctttcagttatatgtgttttactcgtttttgcatcccttttcagatactggaaaatccactgtgatgtacgcttctgttgctttttgttccacgacagataactgacataatttatcctcgataaag

upper sequence: Vv01s0011g01870.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G454412_T01 (Zea mays), 5'ss of exon 1
GTTGGTCAACCCCCGGAGAATTGGACTAGTGGAGTAGATCTTGGACGTCTTCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAGgtttgtagttttgaat-cgccaaatcgtctttagcatttatt--tttggtagcctgtttatgtttgattacctttaaatggagaggcaggctt--attacccagc------------------------------
  ||  ||   |||  | |||||||| |||||||| |||||||| || ||||| || |  || |||||||||||||||| ||||||||||   ||  |||||| |   ||||   | |    |||  | | |    |||| |  |||  |   |  |||     |  |      |  |  | || | | ||||  ||| |                                   
TGTGACCATGGCCCTCAAAATTGGACCAGTGGAGTTGATCTTGGCCGCCTTCTGGATCGTCTTGAACTTGATCTTATCATAACCAGCGAATCACTCAAAGgttcggcattttccttgctttcaattatatatgtgttttactcgttttttcatcccttttcagatactggaaaatccactgtgatgtacgcttctattgctttttgttccatgacataatttatcctcgataaag

upper sequence: Vv01s0011g01870.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G020210_T01 (Zea mays), 5'ss of exon 1
GTTGGTCAACCCCCGGAGAATTGGACTAGTGGAGTAGATCTTGGACGTCTTCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAGgtttgtagttttgaat-cgccaaatcgtctttag----catttatttttggtagcctgtttatgtttgattacctttaaatggagaggcaggcttattacccagc-----------------------------------------
  ||  ||   |||  | |||||||| |||||||| |||||||| || ||||| || |  || |||||||||||||||| ||||||||||   ||  |||||| |   ||||   | |    | |  | | |       | |  ||||||    ||| || |  |      |  |  |    || |  |     | || |                                              
TGTGACCATGGCCCTCAAAATTGGACCAGTGGAGTTGATCTTGGCCGCCTTCTGGATCGTCTTGAACTTGATCTTATCATAACCAGCGAATCACTCAAAGgttcggcattttccttgctttcagttatatatgtgttttactcgtttttgcatcccttttcagatactggaaaatccactgtgatatacgcttctgttgctttttgttccacgacagataactgacataatttaacctcgataaag

upper sequence: Vv01s0011g01870.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA07G34800.1 (Glycine max), 5'ss of exon 5
GTTGGTCAACCCCCGGAGAATTGGACTAGTGGAGTAGATCTTGGACGTCTTCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAGgtttgtag-ttttgaatcgccaaatcgtctttagcatttatttttggtagcctgtttatgtttgattacctttaaatggagaggcaggcttattacccagc---
|||||||||||||| || |||||||| |||||||| |||||||| || |||||||| ||||| ||||||||||| || ||||| |  ||||  || ||||||||| |    || | |    ||      |  | |||| | || |   |     |    || | |  |   |  | |   ||  | |  |||||      |   
GTTGGTCAACCCCCCGAAAATTGGACAAGTGGAGTTGATCTTGGCCGACTTCTTGATCTCCTTGAACTTGATCTCATTACAACAAATGAAGCACTCCAAGgtttgcaaacattcagttattaa--taattcaaacattcaattctctcaattaatagcagtattaaaaggctgcagtattga--ctgttttattgtttcacaat

upper sequence: Vv01s0011g01870.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA20G02500.1 (Glycine max), 5'ss of exon 4
GTTGGTCAACCCCCGGAGAATTGGACTAGTGGAGTAGATCTTGGACGTCTTCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAGgtttgtag-ttttgaatcgccaaatcgtctttagcatttatttttggtagcctgtt-tatgtttgattacctttaaatggagaggcaggcttattacccagc
|||||||||||||| || |||||||| |||||||| |||||||| || |||||||| ||||| ||||||||||| || ||||| |  ||||  || ||||||||| |    || | |    ||      |  |  ||| | || |   |     |   ||  || |    ||  |         |     || || | ||  
GTTGGTCAACCCCCAGAAAATTGGACAAGTGGAGTTGATCTTGGCCGACTTCTTGATCTCCTTGAACTTGATCTCATTACAACAAATGAAGCACTCCAAGgtttgcaaacattcagttattaa--taattcaaatattcaattctctcaattaatggcattattaaaaggctgcagtatttagtgttttattgtttcacaat

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|110698544|gb|EE076162.1|EE076162
EST:     TCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAG                         CTGCAGTGCATGAGCAAATAAATGCTTCAGCGGCAGGGATTGATTCTACGG
genomic: TCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAGgtttgtagtt ... gtcaatatagCTGCAGTGCATGAGCAAATAAATGCTTCAGCGGCAGGGATTGATTCTACGG
EST: gi|30323642|gb|CD006904.1|CD006904
EST:     TCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAG                         CTGCAGTGCATGAGCAAATAAATGCTTCAGCGGCAGGGATTGATTCTACGG
genomic: TCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAGgtttgtagtt ... gtcaatatagCTGCAGTGCATGAGCAAATAAATGCTTCAGCGGCAGGGATTGATTCTACGG
EST: gi|32247297|gb|CD713116.1|CD713116
EST:     TCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAG                         CTGCAGTGCATGAGCAAATAAATGCTTCAGCGGCAGGGATTGATTCTACGG
genomic: TCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAGgtttgtagtt ... gtcaatatagCTGCAGTGCATGAGCAAATAAATGCTTCAGCGGCAGGGATTGATTCTACGG
EST: gi|30326774|gb|CD010036.1|CD010036
EST:     TCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAG                         CTGCAGTGCATGAGCAAATAAATGCTTCAGCGGCAGGGATTGATTCTACGG
genomic: TCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAGgtttgtagtt ... gtcaatatagCTGCAGTGCATGAGCAAATAAATGCTTCAGCGGCAGGGATTGATTCTACGG
EST: gi|110373462|gb|EC937703.1|EC937703
EST:     TCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAG                         CTGCAGTGCATGAGCAAATAAATGCTTCAGCGGCAGGGATTGATTCTACGG
genomic: TCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAGgtttgtagtt ... gtcaatatagCTGCAGTGCATGAGCAAATAAATGCTTCAGCGGCAGGGATTGATTCTACGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGTCAACCCCCGGAGAATTGGACTAGTGGAGTAGATCTTGGACGTCTTCTTGACCTCCTCGAACTTGATCTTATCACAACCAGCGAAGGGCTTCAAGgtttgtagttttgaatcgccaaatcgtctttagcatttatttttggtagcctgtttatgtttgattacctttaaatggagaggcaggcttattacccagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgga