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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctttgctattattccctttaagtatttaaaattttggcttgaacattcttttttgtggatttatgacctctcccattccattgtttgatggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA

Basic information

species Vitis vinifera
transcript Vv11s0016g02890.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os06g05870.1 (Oryza sativa), 3'ss of exon 2
-----tcctttgctattattccctttaagtatttaaaattttggcttgaacattcttttttgtggatttatgacctctcccattccattgtttgatggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA
        | || |   |     ||    || |  |||||  |   ||  || |      | |    |||||||         |||  || |  |   ||||||| ||| || ||| || ||||| || ||||| |||||||||||  | |||||||| ||| ||||||||||||| || ||||| |||||||| ||||
tgacagagtctgatgaaaggttgttggcttactgcaaattcagttatgttcaattggaagttt---cttatgacacggaatgctcctctgctgaa--attttcagTCTCGTGGGATTGATCACCTTGTTATTCCTACAAGAGATTATATGTTTGCTCCCTCACTTGTGGATATTAGTCGAGCTGTTGATTTCATACATA

upper sequence: Vv11s0016g02890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G051288_T01 (Zea mays), 3'ss of exon 2
-tcctttgctattattccctttaagtatttaaaattttggcttgaacattcttttttgtg-gatttatgacctctcccattccattgtttgatggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA
 | | |   ||||||     || ||  || |      |   ||||||  |  |   | ||  ||     | |      |    |   |||     ||  |||||| ||||||| || |||||||||||||| |||||||||||||| ||||| |||||||| | |||||||   |  ||  |||||||||| ||| 
ttgcatgtatattatgttggttcagagttcaggggactcaattgaactcttgtgcatatgcaatgcgaaaacatgtataaataacaatttctc--ttaccagGCTAATGAGATTGAGCACCTGGTAATTCCAACAAGAGATTACCTCTTTGCACCTTCATTCGAGGATATTTCTCAAGCCATAGATTTCATCCATC

upper sequence: Vv11s0016g02890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G863550_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------tcctttg---ctattattccctttaagtatttaaaattttggcttgaac-attcttttttgtggatttatgacctctcccattccattgtttgatggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA
                                                                | | ||    ||   ||   |     | |    || |  || |   | | ||| |   |     ||         |    || |   | |       ||| ||| | | || ||| || ||||| || ||||| |||||||||||  | |||||||||||| ||||||||||||  |  |||   |||||||||||||
gtaagttattttcccttttcatgctgaaaaatttatgttgtttcacggatccttaattcaaagtttcattaaaccttgcatatgccaccgggaacagaactgctgacccaatctattttcaatcagaaatacgctgtgacctaaatgctcctctgctgaaatttacagTCACGTGGGATCGATCACCTTGTTATTCCTACAAGAGATTATATGTTTGCTCCTTCACTTGTGGATATTAATCAAGCTACTGATTTCATTCATA

upper sequence: Vv11s0016g02890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G36020.1 (Glycine max), 3'ss of exon 2
tcctttgctattattccctttaagtatttaaaattttggcttgaacattcttttttgtggatttatgacctctc--ccatt--ccattgtttgatggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA
   ||||   ||| |   |  |   ||  | | |||     || |  ||  | | | ||  |||| ||    |   |||||    ||   ||| |   ||||||||||| | ||| || ||  |||| |||||||| |||||||| || ||||| || |||||||||||||| | ||| |||||  | ||||||||| 
---tttgtgtttaatggatacagaaata-atagtttcacaatgtattttagtatatttgtttttaggagaaatagaccattgatgatatcttggtttgtttcagGCTCACGGGATTGATCATTTGGTGATTCCCACCAGAGATTATCTCTTTGCCCCCTCATTTGTGGATATCAACCGGGCTGTGCAGTTCATTCATC

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|156735982|gb|EV240103.1|EV240103
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|351032518|gb|FQ458883.1|FQ458883
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|161719492|gb|FC067690.1|FC067690
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|351034943|gb|FQ458300.1|FQ458300
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|349809160|gb|FQ398901.1|FQ398901
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|352791479|gb|FQ481058.1|FQ481058
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCCCATGAGATAGACCAC
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCAC
EST: gi|351039844|gb|FQ464882.1|FQ464882
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|110379170|gb|EC944349.1|EC944349
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|71876810|gb|DT025865.1|DT025865
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|351044066|gb|FQ452739.1|FQ452739
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|110388085|gb|EC952801.1|EC952801
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|351037982|gb|FQ465220.1|FQ465220
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|351052950|gb|FQ453937.1|FQ453937
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|349819705|gb|FQ402642.1|FQ402642
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|351037230|gb|FQ457063.1|FQ457063
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|351038655|gb|FQ464521.1|FQ464521
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|351056738|gb|FQ443365.1|FQ443365
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|71856681|gb|DT005736.1|DT005736
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|351041750|gb|FQ455960.1|FQ455960
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|351041720|gb|FQ455930.1|FQ455930
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|30304523|gb|CB981317.1|CB981317
EST:     TTACTTTAAATGAACCTTATGATACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|351038816|gb|FQ464682.1|FQ464682
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|110729962|gb|EE106494.1|EE106494
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|349818207|gb|FQ408982.1|FQ408982
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAAATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|349823003|gb|FQ399982.1|FQ399982
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|351037592|gb|FQ462575.1|FQ462575
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|349822165|gb|FQ412429.1|FQ412429
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAC                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
EST: gi|110689256|gb|EE065319.1|EE065319
EST:     TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCAT                         GCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT
genomic: TTACTTTAAATGAACCTTATGAAACTTTGGTTCCCACGTCCTTGTATCATgtgagtggtt ... tggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcttttttgtggatttatgacctctcccattccattgtttgatggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA
                                       gtttgat  putative branch site (score: 5)
                                                ttttc  putative PPT
     ttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctttgctattattccctttaagtatttaaaattttggcttgaacattcttttttgtggatttatgacctctcccattccattgtttgatggttttcagGCTCATGAGATAGACCACCTGGTAATTCCCACAAGAGATTACCTTTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA

-cctttgc
- - - - - - - -cccttta
- - - - - - - - - - - - - - - - - - tggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtgga