Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatttttcgtaaatgatgaggtctcgcttacaatttttatgggcgatttcttatgggaatttatgatttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA

Basic information

species Vitis vinifera
transcript Vv08s0007g01980.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 2
gtattatttttcgtaaatgatgag---gtctcgcttacaattttta--tgggcgatttcttatgggaatttatgatttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA
||||     || | || |  |      || |  | | |  | | ||  ||   |  || |  ||   |  | |  || || | |||||||||||| || ||||| ||||||||||| || ||||||||  ||||||| ||| | ||||| |||| ||| ||| || |
gtat-gcagtttgcaagtcttccatttgtttgacctgccctgtgtaactgattgtgttgtactgacgagctgttcttcgtgt-agCCAAGGAGCATGTTGTTGGCTGGTACAGCACCGGTCCAAAACTCAGGGAGAACGACTTGGATATACACGCACTATTCAATAA

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G368908_T02 (Zea mays), 3'ss of exon 2
-------gtatta--tttttcgtaaatgatgaggtctcgcttacaatttttatgggcgatttcttatgggaatttatgatttgt--ttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA
       |||| |   || |||       |  || ||    |    | |  ||       | || ||| | ||      |||||  | ||||||||||||| || ||||| ||||||||||| || ||||||||  ||||||||||| | ||| | || | | ||||| |   
gtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAG

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 2
-------gtattatttttcgtaaatgatg--aggtctcgcttacaatttttatgggcgatttcttatgggaatttatgatttgt--ttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA
        ||| |   | |  ||||  ||   || ||         | ||  |       | || ||| | |       |||||  | ||||||||||||| || ||||| ||||||||||| || ||||||||  ||||||| ||| | ||| | || | | | ||| |   
gtatgctctatcaaaatcctcaaattttgttgggcctgatccgtgctattgcttcttttgtcctgatgagcacgggctgtttgtggtgcagCCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAACGACTTGGATGTCCATGCATTATTCAACAG

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 2
gtattatttttcgtaaatgatgag-gtctcgcttacaat-ttttatgggcgatttcttatgggaatttatgatt-tgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA
||||| | |   | || |||||    |   | |||  |  || ||        | ||| |   | |   |  ||   |||||||||||||||| || || || |||||||||||||| || ||||| || ||||||||  | ||| ||||||   ||||| ||| 
gtattttctcaggaaactgatgcttatactgtttatgacattgtagaaatccatgcttttaacactacctacttgcttttcagCCAAGGAGCATGTTGTAGGTTGGTACAGCACAGGCCCTAAACTTCGAGAGAATGATTTGGATGTTCACGCGTTGTTCAATGG

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ23777 (Selaginella moellendorffii), 3'ss of exon 2
gtattatttttcgtaaatgatgaggtctcgcttacaatttttatgggcgatttctt-atgggaatttatgatt-tgttt-cagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA
                                   || || |  | |   ||||||     |   ||| | || || || |||| ||||||||||| ||||||||||||||||| || || ||||| || ||||| || || || |||||||  || ||     |
---------------------------------gtaagttcttcgtgttttttctttgcttggcattacgtttgtgcttgcagCGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAA

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ21414 (Selaginella moellendorffii), 3'ss of exon 2
gtattatttttcgtaaatgatgaggtctcgcttacaatttttatgggcgatttctt-atgggaatttatgatt-tgttt-cagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA
                                   || || |  | |   ||||||     |   ||| | || || || |||| ||||||||||| ||||||||||||||||| || || ||||| || ||||| || || || |||||||  || ||     |
---------------------------------gtaagttcttcgtgttttttctttgcttggcattacgcttgtgcttgcagCGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAA

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|71862429|gb|DT011484.1|DT011484
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGGACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|161713904|gb|FC062870.1|FC062870
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|71861116|gb|DT010171.1|DT010171
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|110689439|gb|EE065663.1|EE065663
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|30125091|gb|CB910430.1|CB910430
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|110697690|gb|EE074900.1|EE074900
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|37188068|gb|CF607419.1|CF607419
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|30297109|gb|CB973903.1|CB973903
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|37188648|gb|CF607997.1|CF607997
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|294965591|gb|GW837190.1|GW837190
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|71864815|gb|DT013870.1|DT013870
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|294967321|gb|GW836675.1|GW836675
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|110713466|gb|EE089412.1|EE089412
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|110711679|gb|EE088432.1|EE088432
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|71859938|gb|DT008993.1|DT008993
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|110687327|gb|EE064641.1|EE064641
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|37186349|gb|CF605702.1|CF605702
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|161712650|gb|FC062222.1|FC062222
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|110718297|gb|EE094970.1|EE094970
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAGTG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|71864932|gb|DT013987.1|DT013987
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAGGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|29783602|gb|CB349901.2|CB349901
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|18459292|gb|BM437570.1|BM437570
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|110690336|gb|EE067344.1|EE067344
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|33406603|gb|CF212230.1|CF212230
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|110401013|gb|EC967604.1|EC967604
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|71861505|gb|DT010560.1|DT010560
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCG
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCG
EST: gi|161710636|gb|FC059390.1|FC059390
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGG
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGG
EST: gi|161721407|gb|FC070435.1|FC070435
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
EST: gi|110712994|gb|EE088527.1|EE088527
EST:     TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG                         CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA
genomic: TGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatttt ... tttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcgcttacaatttttatgggcgatttcttatgggaatttatgatttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA
   cgcttac  putative branch site (score: 3)
                                             tttgtttc  putative PPT
                                    aatttatgatttgttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatttttcgtaaatgatgaggtctcgcttacaatttttatgggcgatttcttatgggaatttatgatttgtttcagCCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA