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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgttcctctctctctctttccaccccccctcccccgttttcctttttctctttgacctattgttgtcatgtttgccaagatcattgtgtctgta...

Basic information

species Vitis vinifera
transcript Vv09s0054g00890.t01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 17
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgta----cgatgttcctctctctctctttccaccccccctcccccgttttcctttttctctttgacctattgttgtcatgtttgccaagatcattgtgtctgta
|||||| |||||||| || ||||||||||| ||||||||||||||||| ||||| |||||| |||  || || |||||||||      | ||   | |  | ||| || |  ||     ||     || |        ||||||  |    || | | || ||   |     |   |  ||| 
ATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGgtaaatctaacgtgtttttaccactcctttcgtccttgaaccttaaattactcaagcaactttgatttgaaatt-tgaagtatg---aacctgtgaagaatgtt

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 17
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgttcctctctctctctttccaccccccctcccccgttttcctttttctctttgaccta--ttgttgtcatgtt-tgccaagatcatt--gtgtctgta
|||||||||||  ||||| |||||||| || ||||||||||||||||| ||||| |||||| | |  ||||| |  ||||||  ||  || | |  |     ||| |       |  ||  ||||| ||           ||||  |   |   |  |  |||||| |   |    |   ||| 
ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgta-aattctcttgttccaggaattcgataat---ttgccaattttctttagaaaaccaatcctagctgactagaaaatcatgccaaaactttccaataattgt-

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 17
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgttcctctctctctctttccaccccccctcccccgtt-ttcctttttctctttgacctattgttgtcatgtttgccaag-atcattgtgtctgta
|||||||||||||||||| |||||||| || ||||||||||||||||||||||| || ||| | |  ||||| ||||||||| | |  ||  ||  |  |  |||         |       | ||  |  | |   |||   |    |  ||| |    |  |  |   || ||  ||| 
ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagct-ctcaactagcagtacttctgtaatttttgagtaaatgtttttcctgcagattgttttgcaatgatcaaggaaacttattaaacttctgattgt-

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM2G128877_T04 (Zea mays), 5'ss of exon 1
---------------------ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgttcctctctctctctttccaccccccctcccccgtt-ttcctttttctctttgacctattgttgtcatgtttgccaag-atcattgtgtctgta
                     |||||||||||||||||| |||||||| || ||||||||||||||||||||||| || ||| | |  ||||| ||||||||| | |  ||  ||  |  |  |||         |       | ||  |  | |   |||   |    |  ||| |    |  |  |   || ||  ||| 
ACAAGTGTTGTTTAATATTAGATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagct-ctcaactagcagtacttctgtaatttttgagtaaatgtttttcctgcagattgttttgcaatgatcaaggaaacttattaaacttctgattgt-

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 17
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgta-------cgatgttcctctctctctctttccacc--ccccctcccccgttttcctttttctctttgacctattgttgtcatgttt-gccaagatcattgtgtctgta
|||||||||||||||||| |||||||| || ||||||||||||||||| ||||| || ||| | |  ||||| |||||||||         |||  |  | | || | ||   |||   |   |  | |  |||  | || |||      ||||  ||||  ||||| | ||||||  |||        
ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACATTATTCACTTCAACACATTGGCAAATCAGgtaaggtctttaatgcccacccccctgttttgtaaccaatcaattatcacaatttattgttgctccacctgctatcattgtattgttttgtcaagat--ttg--------

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 18
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgttcctc----tctctctctttccaccccccctcccccgttttcctttttctctttgacctattgttgtcatgtttgccaagatcattgtgtctgta
|||||| || |||||||||||||||||||| ||||||||||||||||| |||||||||||||| |||||||| ||||||||| | || |        ||   |  |||                 ||                  | || ||  ||||      | || |    ||  ||   
ATATGACAAATTCTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAGgtatggtggtgtaaggaatcaggcagtttttggtgttttatttatattagaaaaaagaagaaaagtccat-gtaatcattggcatctaggttcaagttact---

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 18
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgttcctc----tctctctctttccaccccccctcccccgttttcctttttctctttgacctattgttgtcatgtttgccaagatcattgtgtctgta
||||||||| || ||||||||||||||||| ||||||||||||||||| |||||||||||||| |||||||| ||||||||| | |  |        ||   |  |||                  |                  | || ||  ||||      | || |    ||  ||   
ATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAGgtatggtagtgtaaggaatcaggcagtttttggtgttttatttatactagaaaaaagaagaaaagtccat-gtaatcattggcatctaggttcaagttact---

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 18
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgttcctctctctctctttccaccccccctcccccgttttcctttttctctttgacctattgttgtcatgtttgccaagatcattgtgtctgta---
|||||| || ||||| || ||||||||||| || ||||||||||| || |||||||||||||| ||  | ||||| ||||||  ||         | | |   | |    |          ||    |   |   |||| |    |     |   ||       ||  || ||  |  |   
ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAGgta-aataagatgagatttatacatactatgctaagtggggattaaggtcaattggtttgtctaggtaaaaacccatt------aattgttttggatacacag

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 18
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgta----cgatgttcctctctctctctttccaccccccctcccccgttttcctttttctctttgacctattg--ttgtcatgt-------ttgccaagatcattgtgtctgta----------------------------------------------------------------
 ||||| || |||||||| ||||||||||| || ||||||||||| |||||| |||| ||| | | | | || ||||||||     || | ||||    | | | | |  |       ||      |   ||||||    ||||   |||   |||| |  |       |||   | ||  |  ||  ||                                                                  
TTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAGgtttgctcgttattccaaaatgtttttgtttattatttatcttttcctcctcttttttgaattgattcattaatttgttaaatctttgagttgttcaaattttgatgattgggtggttgtatctcaactcgtatgtttacaaattccaaaactaatgagcgatgatttcatctgcag

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 18
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgttcctctctctctctttccaccccccctcccccgttttcctttttctctttgacctattgtt-gtcatgtttgccaagatcattgtgtctgta
 ||||||||||||||||| ||||| || || || |||||||||||||||||| |||| ||  | | | | |||||||||||       ||       |||   |  ||         |  ||||| |   |  |   ||  ||    || ||  |   |  |  |||||   ||| |   
TTATGATAAGTTCTGCCCATTCTATAAATCAGTATGGATGATGCGCAATATTGTCCACTTTAACACTCTTGCCAATCAGgtctttctctcactcgattcttactgtacagttggcatcaagtttttccggtcattactgctcttcaattagttgttcatatcttgatcaacatgtttac-

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: EFJ33015 (Selaginella moellendorffii), 5'ss of exon 17
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgttcctctctctctctttccaccccccctcccccgttttcctttttctctttgacctattgttgtcatgtttgccaagatcattgtgtctgta
||| |||||||| || || ||||||||||| |||||||||||||| || ||  | |||||||   |  || ||| |||||||   ||  |  |  |  |||||||     |  |        ||| |||| |||    |                                        
ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAGgta---tgcactgccatacctctttca----cgtccttgaaaatttactttctcttgcag----------------------------------------

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 18
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgttcctctctctctctttccaccccccctcccccgttttcctttttctctttgacctattgttgtcatgtttgccaagatcattgtgtctgta
||| |||||||| || || ||||||||||| |||||||||||||| || ||  |||||||||   |  || ||| |||||||   ||  |  |  |  |||||||     |  |       |||| |||| |||    |                                        
ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAGgta---tgcactgccatacctctttca----cgtccttgaaattttactttctcttgcag----------------------------------------

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|22010913|gb|BQ795947.1|BQ795947
EST:     GCAATATTATCCATTTCTATAATTTGGCCAATCAG                         GCAGTAGAGCGTGGAGCTGGTATGGATGGACAGAAGATAACTTACACCCTT
genomic: GCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgtt ... aaatatacagGCAGTAGAGCGTGGAGCTGGTATGGATGGACAGAAGATAACTTACACCCTT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgttcctctctctctctttccaccccccctcccccgttttcctttttctctttgacctattgttgtcatgtttgccaagatcattgtgtctgta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccccc