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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCAATATTGGAGAGGGAGGTATTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcactaaagctactgtatgatttttggtctcgtgttcactcatgccttgtgttgctacatatccatgcatctatgttcattaacttcattcatgc...

Basic information

species Vitis vinifera
transcript Vv08s0040g01700.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g01700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 7
CTGCAATATTGGAGAGGGAGGTATTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcactaaagctactgtatgatttttggtctcgtgt-tcactcatgccttgtgttgctacatatccatgcatctatgttcattaacttcattcatgc-
 ||||||||||| || || || |||  ||| || ||||| |||||||||||||| || ||||||||||| ||||| ||    |  | | | | | || ||| |    |  | | |      |   ||||| |    |||    ||| |      ||   |   ||    || |  
TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtcttggaacaatt-tctgctttctaccataatttgttgtgttttatttgtggtttctcatgat-atgtaagggaattttgtgttttttcccaaggc

upper sequence: Vv08s0040g01700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G404855_T01 (Zea mays), 5'ss of exon 7
CTGCAATATTGGAGAGGGAGGTATTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcactaaagctactg-tatgatttttggtctcgtgttcactcatgccttgtgttgctacatatccatgcatctatgttcattaacttcattcatgc-
 ||||||||||| || || || |||  ||| || ||||| |||||||||||||| || ||||||||||| ||||| ||    |  | |   |  |    | |    |  | | ||   |  | | |||||| | | || ||  ||   |    | |  ||    |  |||| |  
TTGCAATATTGGTGAAGGTGGCATTTGTCTAGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgagatcttggaacagtttctgctgtctaccataacttattgtgttttac-ttgtgtggtttcacata-atatgttagagatttttgtgatttttcaaggc

upper sequence: Vv08s0040g01700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA13G20790.1 (Glycine max), 5'ss of exon 6
CTGCAATATTGGAGAGGGAGGTATTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcactaaagctactgtatgatttt-tggtctcgtgttcactcatgcct-tgtgttgctacatatccatgcatctatgttcattaacttcattcatgc
|||||| ||||| |||||||||||||| |||||||| || || |||||||| ||||| ||||||||||||||||| ||     ||||      | | |  || |  | ||  |   |  | | | | ||   || |        |||    | | ||||  |  ||  |||||  
CTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAGgtaagctgtgaaagtactcattttaccttatattatccggcctaaaccttcttgtgccctgttgtcatggaatgtgaattttttcaagagattgtttcat--

upper sequence: Vv08s0040g01700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA10G06590.1 (Glycine max), 5'ss of exon 6
CTGCAATATTGGAGAGGGAGGTATTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcactaaagctactgtatgatttttggtctcgtgttcactcatgccttgtgt--tgctacatatccatgc-atctatgttcattaacttcattcatgc
|||||| ||||| ||||| |||||||| |||||||| || || |||||||| ||||| ||||||||||||||||| ||     |||       |   |  ||   |    ||| |       | ||||||  || |        |||  |  | | || |  |  ||  ||||   
CTGCAACATTGGTGAGGGCGGTATTGCACTTGCTGAGGCTGTACATGGTTCAGCACCTGATATTGCTGGAAAGgtgagctgtgaaaatactcattctaccttatattgtctgtcctaaacctctttgtgtcctgttgtcatggaatgtgaaatttttttaagaggttgtttca---

upper sequence: Vv08s0040g01700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA10G06590.2 (Glycine max), 5'ss of exon 5
---------------------------CTGCAATATTGGAGAGGGAGGTATTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcactaaagctactgtatgatttttggtctcgtgttcactcatgccttgtgt--tgctacatatccatgc-atctatgttcattaacttcattcatgc
                           |||||| ||||| ||||| |||||||| |||||||| || || |||||||| ||||| ||||||||||||||||| ||     |||       |   |  ||   |    ||| |       | ||||||  || |        |||  |  | | || |  |  ||  ||||   
TCTGAGAATGTTTTATGTCTTTTGCAGCTGCAACATTGGTGAGGGCGGTATTGCACTTGCTGAGGCTGTACATGGTTCAGCACCTGATATTGCTGGAAAGgtgagctgtgaaaatactcattctaccttatattgtctgtcctaaacctctttgtgtcctgttgtcatggaatgtgaaatttttttaagaggttgtttca---

upper sequence: Vv08s0040g01700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT3G09810.1 (Arabidopsis thaliana), 5'ss of exon 6
CTGCAATATTGGAGAGGGAGGTATTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcactaaagctactgtatgatttttggtctcgtgttcactcatgccttgtgttgctacatatccatgcatctatgttcattaacttcattcatgc-
    |||||||| ||||  |||||||| ||||||||||| ||||| || |||||||| ||||||||||||| |||||||||  |    ||   | | ||  | | |||    |    | |||| | | |||| |    |    |  |  |||     | ||    ||| |  | 
TATGAATATTGGGGAGGATGGTATTGCCCTTGCTGAAGCTGTTCACGGCTCTGCACCTGATATTGCTGGAATGgttagtcatcattcttag-atgttatcatcgttctaaattcgtttgatgcatagagttgttgttaacttgttaaattattagagtaaataggatttagaca

upper sequence: Vv08s0040g01700.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 5'ss of exon 6
CTGCAATATTGGAGAGGGAGGTATTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcactaaagctac-------------tgtatgatttttggtctcgtgt---tcactcatgccttgtgttgctacatatccatgcatctatgttcattaacttcattcatgc----------------------
 || ||||||||||| |  ||| | || ||||||||||| ||||| ||||||||||| ||||| |||||||||||| |||  | || | |              |  || ||||  || ||   |    ||| | |||| |    |    | | ||  ||  || | || |  |||| ||  ||  ||                       
TTGTAATATTGGAGAAGATGGTGTAGCCCTTGCTGAAGCAGTTCACGGTTCTGCACCTGATATCGCTGGAAAGgttggtccttcaaacaatatatcattccaatttcatcatttacgggctaaagagtatcatttatgcatccaatgttgaaagattaat--atgtgtgatttttaaatttgttgttgtctttctgttttgggtgatgtag

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|110723902|gb|EE099271.1|EE099271
EST:     TTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAG                         AATATGGCAAACCCAACTGCTTTGATGTTGAGTGCTGTTCA-AATGCTTCC
genomic: TTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcact ... cattttgtagAATATGGCAAACCCAACTGCTTTGATGTTGAGTGCTGT-CACAATGCTTCG
EST: gi|351019648|gb|FQ439465.1|FQ439465
EST:     TTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAG                         AATATGGCGAACCCAACTGCTTTGATGTTGAGTGCTGTCACAATGCTTCGC
genomic: TTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcact ... cattttgtagAATATGGCAAACCCAACTGCTTTGATGTTGAGTGCTGTCACAATGCTTCGC
EST: gi|110712688|gb|EE087955.1|EE087955
EST:     TTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAG                         AATATGGCAAACCCAACTGCTTTGATGTTGAGTGCTGTCACAATGCTTCGC
genomic: TTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcact ... cattttgtagAATATGGCAAACCCAACTGCTTTGATGTTGAGTGCTGTCACAATGCTTCGC
EST: gi|27585749|gb|CB008444.1|CB008444
EST:     TTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAG                         AATATGGCAAACCCAACTGCTTTGATGTTGAGTGCTGTCACAATGCTTCGC
genomic: TTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcact ... cattttgtagAATATGGCAAACCCAACTGCTTTGATGTTGAGTGCTGTCACAATGCTTCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCAATATTGGAGAGGGAGGTATTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcactaaagctactgtatgatttttggtctcgtgttcactcatgccttgtgttgctacatatccatgcatctatgttcattaacttcattcatgc

- - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA