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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctattgacatttttttttaaaattatgccttaaataagcaatttagttcccctatattatggttccttgtatgattgttgatctgaaattgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG

Basic information

species Vitis vinifera
transcript Vv18s0089g00350.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
------cctattgacatttttttttaaaattatgccttaaataagcaatttagttcccctatattatggttccttgtatgattgttgatctgaaattgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG
      | ||     |   | || ||   || |   |   || ||  | ||| ||||  |      ||     |    |||    |||||         ||   ||||||| ||||  || |||||||| || || |||||||||||| |||||||||| || ||||| ||||| |||||||| || ||||| || |||||||| |
atgttccttaagataaacatgttgtattgttgttgttggcatgagttacttacttccatt------tgacctttcaattgacatctgatccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 18
--cctattgacatttttttttaaaattatgccttaaataagcaatttagttcccctatattatggttccttgtatgattgttgatctga--aattgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG
  | |||  || | ||    |        ||| | | ||     |||   |     | |      ||  ||| ||      |||    |  | |  |  || ||||||| |||| ||| |  ||||| || || |||||||||||||| ||||||||||||||||| ||||| ||||| || || ||||| |||||| |||| |
ctcatatcaacctgttccactttcccacggccatgattattt--tttgaatgtgtcaaacacaaatt--ttgaattgcctgtgacacaattactctcccttaagGATACGATGGCCCGGAAGCCTGCTGATCCTGAAGAAGAACTTCGGTGGATGTCTCAAGAAGTTCGTGGTTATGTAGAGGCTGTTTTGAACAGTTTGGCAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM5G870253_T01 (Zea mays), 3'ss of exon 2
cctattgacatttttttttaaaattatgccttaaataagcaatttagttcccctatat-tatggttccttgtatgattgttgatctgaaattgcttttc------agGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG
     |   || ||   | ||   ||   | |   |   || || | |    | | |   | | |  ||| | | | | || ||   | |   ||||||      ||||||||||||  || || ||||| || || |||||||||||||||||||||||||||||||| ||||| ||||||||||| ||||| |||||| ||||||
-----ttttatcttacctaaaggctaaagcatgtttt--catttaaatgtatccaaacacaagatcacttattttactcttcattctacaactcttttctgtttaagGATACAATGGCTCGGAGGCCTGCTGATCCTGAAGAAGAACTTCGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTTTGAACAGTTTGGCTG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 18
--------------------------------------------------------------------------------------cctattgacatttttttttaaaat------tatgccttaaataagc-aat-ttagttcccctatattatggttccttgtatgattgttgatctgaaattgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG
                                                                                         ||   ||| |  ||| |          |||   ||  ||  || ||| | | |     |  ||||   | |      | |    ||| |  | |||  |    ||||||| ||||  || |||||||| || || |||||||||||| ||||||||||||||||||| ||||| ||||| || || ||||| || |||||||| |
gtaagttctagattaatacataattgtattgcatttctagctttcttttgtcgttttgctctactcaactaaatcatgatttattaaggatcatcatgtaatttcaggtccccttgtatattttggatgtgccaatataaatatttttccattaaaatacacaaactaacatctgaccatacatttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------------------------------cctattgacatttttttttaaaat------tatgccttaaataagc-aat-ttagttcccctatattatggttccttgtatgattgt-tgatctgaaattgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG
                                                                                          ||   ||| |  ||| |   |      ||||  ||  ||  || ||| | | | |  ||  ||||   | |      | |   | |||||  | | |  |    ||||| | ||||  || ||||| || || || |||||||||||| ||||||||||||||||||| ||||| |||||||| || ||||| || |||||||| |
gtaagttctaggttaatacataattgaattgcatttctagctttccttttgtagttttgctttactcaattaaatcttgatttattagggatcatcatgtaatttcaggttcccttgtatgttttggatgtgccaatataaatactgctccattaaaatacacaaactaaacatctgatcatacacttttcgaaagGATGCTATGGCGCGGAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 18
cctattgacatttttttttaaaattatgccttaaataagcaatttagttccccta--tattatggtt--ccttgtatgattgttgatctgaa-attgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG
   |||||    |   | |||  | | |  ||  |||| ||||| |       ||  | || |  ||  || ||||| ||| |   | || | ||  | | |||||| |||||||  ||||||||||| ||||| || |||||||| ||||||||||| |||||||| ||||| ||||||||||| |||||||| ||| | ||||
-tgattgag---tcagtctaagctgaggagttgcataa-caattaaaaataaataaatgttgttattgaccatgtattattatatttttgtatatcccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 18
cctattgacatttttttttaaaattatgccttaaataagcaatttagttcccctatattatggttcct-----tgtatgattgt-tgatctgaaattgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG
     | |||   ||    |||   ||   | ||| ||  ||||    | ||  | | | |||||  |     ||||| ||| | |  ||  | ||      |||||| |||||||  ||||||||||| || || || |||||||| ||||||||||| |||||||| ||||| ||||||||||| |||||||| ||| | ||||
-----taacaaaattaaaaaaatacataaat-aaagaataaattgttattcctgaaaatgtggttattgactgtgtattattttattttcatatatcctgcctcagGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 18
--cctattgacatttttttttaaaattatgccttaaataagcaatttagttcccctatattatggttccttgtatgattgttgatctgaaattgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG
    |   || |  ||| |||     | ||       || |   |   | |      |||||  |||     | || ||||  |  |    |   |||||||||||  |||||  | | ||| | |||||| ||||| ||| | || |||||||| |||||||| || || ||||||||||| ||| | |||||||| ||||
agggttaagatagctttgtttgggcatgtgaggcgtttaggtt-tccggatgggtggtattacagttttgcct-tggttgtctaatttttttcctttttcagGATAAGATGGTAAGGAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTG

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|33402994|gb|CF208621.1|CF208621
EST:     GAGGCAAAGTCTTTCTGATGGTTCCCTG                         GATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATG
genomic: GAGGCAAAGTCTTTCTGATGGTTCCCTGgtgagttttt ... tgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATG
EST: gi|34364107|gb|CF405692.1|CF405692
EST:     TGAAGGTGGTCTTACCATGAGGCAAAGTCTTTCTGATGGTTCCCTG                         GATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGNATG
genomic: TGAAGGTGGTCTTACCATGAGGCAAAGTCTTTCTGATGGTTCCCTGgtgagttttt ... tgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATG
EST: gi|161719802|gb|FC065762.1|FC065762
EST:     CCACTGAAGGTGGTCTTACCATGAGGCAAAGTCTTTCTGATGGTTCCCTG                         GATACAATGGTCCGAAGACCTGC
genomic: CCACTGAAGGTGGTCTTACCATGAGGCAAAGTCTTTCTGATGGTTCCCTGgtgagttttt ... tgcttttcagGATACAATGGTCCGAAGACCTGC
EST: gi|30251129|gb|CB968862.1|CB968862
EST:     CCTCTGAAGGTGGTCTTACCATGCGGCAAAGTCTTTCTGATGGTTCCCTG                         GATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATG
genomic: CCACTGAAGGTGGTCTTACCATGAGGCAAAGTCTTTCTGATGGTTCCCTGgtgagttttt ... tgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATG
EST: gi|161714373|gb|FC063214.1|FC063214
EST:     CCTCTGAAGGTGGTCTTACCATGCGGCAAAGTCTTTCTGATGGTTCCCTG                         GATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATG
genomic: CCACTGAAGGTGGTCTTACCATGAGGCAAAGTCTTTCTGATGGTTCCCTGgtgagttttt ... tgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATG
EST: gi|37185438|gb|CF604791.1|CF604791
EST:     CCACTGAAGGTGGTCTTACCATGAGGCAAAGTCTTTCTGATGGTTCCCTG                         GATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATG
genomic: CCACTGAAGGTGGTCTTACCATGAGGCAAAGTCTTTCTGATGGTTCCCTGgtgagttttt ... tgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATG
EST: gi|34364376|gb|CF405961.1|CF405961
EST:     CC-CTGAAGGTGGTCTTACCATGAGGCAAAGTCTTTCTGATGGTTCCCTG                         GATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATG
genomic: CCACTGAAGGTGGTCTTACCATGAGGCAAAGTCTTTCTGATGGTTCCCTGgtgagttttt ... tgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcccctatattatggttccttgtatgattgttgatctgaaattgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG
                               tgttgat  putative branch site (score: 4)
                                            ttgcttttc  putative PPT
        tatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctattgacatttttttttaaaattatgccttaaataagcaatttagttcccctatattatggttccttgtatgattgttgatctgaaattgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
cctattg
- - - - - - - - - -aaaatta
- - - - - - - - - - - - - - - - aaataag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccttg