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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttcatattttgtgtatgaaatttctgttaattatgacatacacatatgtaaagcaatattttgatctgttgtatctacggacag

Basic information

species Vitis vinifera
transcript Vv01s0011g05370.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 13
GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttcat--attttgtgtatgaaattt-----ctgttaattatgacatacacatatgtaaagcaat--attttgatctgttgtatctacggacag-
|| || ||||| |||||||||||||| ||||| |||||||||||| | || |||||||||||||||||||| ||||| |||||||  |   ||  | ||  | |||| ||        |   ||    |||   | |   ||||||    ||  |||||||| ||| | | ||      |  
GTGCCTACTGGGTGGAAATTTTTTGGGAACTTGATGGATGCTGGAATGTGCTCAATTTGTGGTGAAGAAAGCTTTGGCACTGgtaattactatgaacttgatctatggaacacaatgacatatagcagtgaataaaatgcatgtaacttcatgcattttgatatgtggcacctctaattatt

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 13
GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttcatattttgtgtatgaaatttctgt-taattatgacatacacatatgtaaagcaatattttgatctgttgtatct-acggacag--------
|| || ||||| |||||||||||||| || || |||||||||||| | || ||||| |||||||||||||| ||||| |||||||   ||    || ||  ||| |  | | |   |    || |||     | |  |    | |  | |||   |||  | |   | ||  |         
GTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatttggcttctggctatcatttctatacatgccaatcacagtagtaaacatgtcaccacctcttgtattgtcatgttagatgggtaaattgtgtt

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 13
GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttcatattttgtgtatgaaatttctgttaattatg---acatacacatatgtaaa-------gcaatattttgatctgttgtatct-acggacag
|| || ||||| ||||| |||||||| || || |||||||||||| | || ||||| |||||||||||||| ||||| |||||||   |     || ||    ||    || ||   || ||    | | |||||   |||||       ||||  | |||   |||| | |   | ||| | 
GTGCCTACTGGATGGAAGTTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatggcttgtggccttgtgggttgtggctatcatttctatacacacaacagtaaacatgtcagcaacctcttgtattgttatgttagatggata-

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA08G04890.1 (Glycine max), 5'ss of exon 13
GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttcatattttgtgtatgaaatttctgttaattatgacatacacatatgtaaagcaatattttgatctgttgtatctacggacag--------------------
||||| || || ||||| || |||||||| |||||||||||||||||||||||| | |||||||||||||||||||| ||||||| || |    | |||  |    |      |  || ||  || | ||  | | | ||    || ||| |    || |||||   ||                       
GTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgtttgctattgcattaagagga---gcaaagtacaactttcaactttattaaaacctagttttaaactttttatcttgtgattattccttgtgcttgtggatag

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 13
GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttcatattttgtgtatgaaatttc----tgttaattatgacatacacatatgtaaagcaatattttg-----atctgttgtatctacggacag
||||| || || ||||| || |||||||| |||||||||||||||||||||||| | |||||||||||||||||||| ||||||| || |    | |||  |    |    |    |   | ||   || |    | |    |     ||| |||     ||   |||| | |  ||| ||
GTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgtttgctattgcattaagaggagcaaagtacaactttcaactttattaaaacctagtttttatcttgtgattattccttgtgtttgtggatag

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA03G05150.1 (Glycine max), 5'ss of exon 7
GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttcatattttgtgtatgaaatttctgttaattatgacatacacatatgtaaagcaatattttgatctgttgtatctacggacag--------------------
||||| || || ||||| || |||||||| |||||||||||| ||||||||||| | |||||||||||||||||||| ||||||| || |    | |||  |   ||      |  || ||  || | ||  | | | ||    || ||| |    || |||||   ||                       
GTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgtttgctattgcattaaaagga---gcaaagtacaactttcaactttattaaaacctagttttaaactttttatcttgtgattattccttgtgtttgtggatag

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 13
GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttcatattttgtgtatgaaatttctgttaattatgacatacacatatgtaaag---caatattttgatctgttgtatctacggacag
|| ||||| |||||||| |||||||||||  | |||||||||||  | |||||  ||||||| |||||||||||||||||||||  ||||| |||||      | | |  |||||| || |    | |   |  | || ||     | |    ||||| |   |           
GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttc-tatttccacactcacacatctgttcataactttaaaacaacctatacagttctgaaagaaagatctttcacag----------

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: EFJ05270 (Selaginella moellendorffii), 5'ss of exon 12
GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttcatattttgtgtatgaaatttctgttaattatgacatacacatatgtaaagcaatattttgatctgttgtatctacggacag
||||| ||||| ||||| |||||||| ||||| |||||||||||  | ||||| || ||||||||||||||||| ||||| ||||  | |      ||   |  ||||||  ||||            |   | ||||    | | | |||  || |||||| |     |||
GTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCGgtaactct------ttacattcgaaattagtgtt------------cctgtgtgta---tattgtgttg--cttttgtatttgtttgcag

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: EFJ09195 (Selaginella moellendorffii), 5'ss of exon 12
GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttcatattttgtgtatgaaatttctgttaattatgacatacacatatgtaaagcaatattttgatctgttgtatctacggacag
||||| ||||| ||||| |||||||| ||||| |||||||||||  | ||||| || ||||||||||||||||| ||||| ||||  | |      ||   |  | ||||  ||||  |       |  | || |||   ||  | || |  | | ||| |           
GTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCGgtaactct------ttacattcggaattagtgttcct----gtgtgtatat-tgtgttgc--ttttgtatttttttgcag----------

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|30129214|gb|CB914553.1|CB914553
EST:     AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG                         GTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
genomic: AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttca ... ctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
EST: gi|110388407|gb|EC953157.1|EC953157
EST:     AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG                         GTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
genomic: AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttca ... ctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
EST: gi|30133454|gb|CB918793.1|CB918793
EST:     AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG                         GTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
genomic: AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttca ... ctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
EST: gi|22009717|gb|BQ794751.1|BQ794751
EST:     AA-GGATGCTGGATTATG-TCAA-TTGTGG-GAAGAAAG-TTTGGAACT-                         GTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
genomic: AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttca ... ctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
EST: gi|37188896|gb|CF608245.1|CF608245
EST:     AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG                         GTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
genomic: AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttca ... ctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
EST: gi|32270099|gb|CD719258.1|CD719258
EST:     AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG                         GTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
genomic: AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttca ... ctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
EST: gi|30137874|gb|CB923212.1|CB923212
EST:     AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG                         GTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
genomic: AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttca ... ctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
EST: gi|37183515|gb|CF602869.1|CF602869
EST:     AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG                         GTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
genomic: AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttca ... ctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
EST: gi|46917505|gb|CN546834.1|CN546834
EST:     AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG                         GTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
genomic: AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttca ... ctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
EST: gi|37185226|gb|CF604579.1|CF604579
EST:     AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG                         GTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
genomic: AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttca ... ctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
EST: gi|110694852|gb|EE072334.1|EE072334
EST:     AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG                         GTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
genomic: AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttca ... ctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC
EST: gi|161715091|gb|FC063627.1|FC063627
EST:     AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG                         GTTCGGACCACATTCGTGAGATAGATGGAATCTGGGCTGTTTTAGCTTGGC
genomic: AATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttca ... ctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttcatattttgtgtatgaaatttctgttaattatgacatacacatatgtaaagcaatattttgatctgttgtatctacggacag

- - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA