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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctgaaatttattttttaatggtaaccattttctatttgtaggacattgctaaaattaatggcaagctgtgaataatagctctagatgaacaaa...

Basic information

species Vitis vinifera
transcript Vv13s0019g04680.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 7
GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctgaaatttat----tttttaatggtaaccattttctatttgtaggacattgctaaaattaatggcaagctgtgaataatagctctagatgaacaaa---
|| |     || |||||||||||||||  |||| | || || || ||||| ||||||||||||||||| ||||||||  | |||||||||   ||   |   |||     | ||     | || || | | |   | |||| |  ||||| |  |    || |||    ||  ||  || |  | | |||    
GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAGgtatgccccctagcatatgaagctatttgctttcacgatgtccaagaagcaggata--gctaacaagag-aacatgct----attttatttcaaattaatcaagctg

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 8
GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctgaaatttattttttaatggtaaccattttctatttgtaggac-attgctaaaattaatggcaagctgtgaataatagctctagatgaacaaa-----
||||     || || |||||||||||   |||||| || ||||| || || || |||||||||||||| |||||||| ||||||||||||     |||  |  ||     |||| |     |     |  || | ||  |     ||   ||   |||| |||| |||  ||  ||||  | |  |||     
GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttgag-tgcatga---aatgtttgttttacataacatgcaagaggagaagcaattctagctgcaa-ctgttaatgtta-ttctactttagaaaagatca

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM5G863105_T01 (Zea mays), 5'ss of exon 3
GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctgaaatttattttttaatggtaaccattttctatttgtaggac-attgctaaaattaatggcaagctgtgaataatagctctagatgaacaaa----
||||     || ||||||||||||||    ||||| || ||||| || || || |||||||||||||| |||||||| ||||||||||||     |||| |  ||    |  | ||     |     |  |||| ||  |     |||  ||   |||| |  | |||  ||    |   | || | |    
GATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAGgtatgctttgaa-tacataaactgtttgt---tttacataacatgtaagatgagaaacaaatctagctgcaa-ccattaatgctattcttgtttaaaaagaccag

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA10G35230.2 (Glycine max), 5'ss of exon 7
GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctgaaatttattttttaatggtaaccattttcta---tttgt-aggacattgctaaaattaatggcaagctgtgaataatagctctagatgaacaaa
||||| | ||| ||||||||||||||||||||||| || || || ||||||||||||||||| ||||| |||||  | ||||||||||||  |  |||  |||  ||  | |  || |  |  || ||   ||  | | ||||||  |   |||  |||||||                            
GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtt-tgatgttttcttccttacagttattagattataaaattaatcatgacatt--ttgtatt--tggcaag----------------------------

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA10G35230.1 (Glycine max), 5'ss of exon 7
GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctgaaatttattttttaatggtaaccattttcta---tttgt-aggacattgctaaaattaatggcaagctgtgaataatagctctagatgaacaaa
||||| | ||| ||||||||||||||||||||||| || || || ||||||||||||||||| ||||| |||||  | ||||||||||||  |  |||  |||  ||  | |  || |  |  || ||   ||  | | ||||||  |  | ||      ||   |    ||  | |  | ||  || |  
GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtt-tgatgttttcttccttacagttattagattataaaattaatcatgacatt-ttgtatttggcaagaatgagaatgtacgaacaatgga-aaatag-

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 7
GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctgaaatttattttttaatggtaaccatttt----ctatttgtaggacattgc---taaaattaatggcaagctgtgaataatagctctagatgaacaaa
||||| | ||| |||||||||||||||| |||||| || || || ||||||||||||||||| ||||| |||||  | ||||||||||||  |       ||| ||  ||   | ||   ||| |     || |  |   |  |||    |   |  ||||  ||  |||||| | |||       |       
GATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtttgatgttttcttccttccagttattgattataaaattaatcatgacattttgtatttggcaagaatgaaaatgtgtgaacagtagaaaatagt-------

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 7
GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctgaaatttattttttaatggtaaccattttct---atttgt-aggacattgctaaaattaatggcaagctgtgaataatagctctagatgaacaaa
                   |||||||||||||||| || || || ||||||||||||||||| ||||| |||||  | ||||||||||||  |  |||  |||  ||  | |  || |  |  || |   |||  | | ||||||  |  | ||      ||   |    ||  | |  | ||  || |  
-------------------AGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAGgtatgtt-tgatgttttcttccttacagttattagattataaaattaatcatgacatt-ttgtatttggcaagaatgagaatgtacgaacaatgga-aaatag-

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 7
GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacat-cctgaaatttattttttaatggtaacc-attttctatttgtaggacattgctaaaat-taatggcaagctgtgaataatagctctagatgaacaaa
||||| || ||   |||||||||||| || |||||||| ||||| || || || |||||||| ||||||||||| || |||||||||||     | |     ||   | | | |  | | | |||||||  |  |  |   ||  | | || | ||     | | |   | || ||| | ||     |  
GATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAGgtgtgcacttctttcttgcctctgatttatgatcgattttcttgtcctctgcatttattgagatcttattatccgtt-tctttcattgctttggaattgga--

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|351049141|gb|FQ449863.1|FQ449863
EST:     TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG                         GAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
genomic: TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctg ... tatctggcagGAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
EST: gi|110378503|gb|EC943640.1|EC943640
EST:     TTATTGAGACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG                         GAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
genomic: TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctg ... tatctggcagGAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
EST: gi|110386522|gb|EC951122.1|EC951122
EST:     TTATTGAGACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG                         GAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
genomic: TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctg ... tatctggcagGAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
EST: gi|110707796|gb|EE084605.1|EE084605
EST:     TTATTGAGACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG                         GAAATTGCTAAAAAATTGCCACGCCCCTCCTCATCGTGATTGCAGATCTTA
genomic: TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctg ... tatctggcagGAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
EST: gi|351029650|gb|FQ427490.1|FQ427490
EST:     TTATTGAGACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG                         GAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
genomic: TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctg ... tatctggcagGAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
EST: gi|351036602|gb|FQ457315.1|FQ457315
EST:     TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG                         GAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
genomic: TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctg ... tatctggcagGAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
EST: gi|110390981|gb|EC955931.1|EC955931
EST:     TTATTGAGACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG                         GAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
genomic: TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctg ... tatctggcagGAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
EST: gi|351033397|gb|FQ462048.1|FQ462048
EST:     TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG                         GAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
genomic: TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctg ... tatctggcagGAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
EST: gi|30302011|gb|CB978805.1|CB978805
EST:     TTATTGAGACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG                         GAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
genomic: TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctg ... tatctggcagGAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
EST: gi|349830843|gb|FQ418151.1|FQ418151
EST:     TTATTGAGACATCTGCAGAGACAGCTGATAACATAAACCAGCTGTTTGAG                         GAGATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
genomic: TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctg ... tatctggcagGAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
EST: gi|110428129|gb|EC994591.1|EC994591
EST:     TTATTGAGACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG                         GAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
genomic: TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctg ... tatctggcagGAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
EST: gi|351016862|gb|FQ424289.1|FQ424289
EST:     TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG                         GAAATTGCTAAAAAATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
genomic: TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctg ... tatctggcagGAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
EST: gi|110691925|gb|EE070587.1|EE070587
EST:     TTATTGAGACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG                         GAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA
genomic: TTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctg ... tatctggcagGAAATTGCTAAAAGATTGCCACGCCCTTCCTCATCGTGATTGCAGATCTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGgtacatcctgaaatttattttttaatggtaaccattttctatttgtaggacattgctaaaattaatggcaagctgtgaataatagctctagatgaacaaa

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattaa