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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaaccatgttggtcatgatatattatgtaatacttttccatctaatatttttccttaaattattatatatctcatgaataatttttctggttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC

Basic information

species Vitis vinifera
transcript Vv18s0001g00480.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os05g48290.1 (Oryza sativa), 3'ss of exon 6
ctaaccatgttggtcatg-atatattatgtaatacttttccatctaatatttttccttaaatt--attatatatctcatgaataattttt-----ctggttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC
       ||||     |  |||  || | ||  ||| |  |||||       |||| ||||||  || | |   || ||    |  ||||     |  |||| |||||| ||||| |  | |||  ||||||| ||||| ||||| || |||||||||||||| |||||||||||||||||| | |||||    || ||||| |||||
--gtttgtgttcacagtacataatttgtctagcactctagcatct------cttccataaattgaatcacaccactaatattcagcttttaattccatgttactgcagATAAGTTTAGATCAGATCTGATGAACATTGCTATGACAACGTTGAGTTCAAAAATACTTTCCCAGGACAAGGAATACTTTGCTGGTCTTGCAGTTGATGC

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 5
ctaaccatgttggt-catgatatattatgtaatacttttccatctaatatttttccttaaattattatatatctcatgaataatttttctggttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC
 |||  ||     | ||     | ||     | |    | | | ||  | | | || | | |  | ||  |||||||||  |  |  | |   |  |||||| |||||||     ||  | ||||| ||||| ||||||||| | ||||||||||| |||||||| ||||||||  | |||||  |||| || || |||||
ataaaaattcaaattcacttcctcttgcaacacatggattcttttagaaatatgccatta-tgctcatcgatctcatgacaatatccttttccttctgcagATAAGTTCAGAGCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTTGCTGAACTTGCGGTTGATGC

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 14
ctaaccatgttggtcatgatatattatgtaatacttttccatctaatatttttccttaaattattatatatctcatg--aataatttttctggttaat--gcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC
  |  ||  ||   ||    || ||   |   |    | |    |  | | | ||   | |    ||  ||||||||  |||| | ||| |  ||  |  ||||| || ||||  |  ||  | ||||| ||||| ||||||||| | ||||||||||| |||||||| ||||||||  | || ||  |||| || || |||||
ggattcaaatt---cacttcatcttgcatctcatggattctctcaggaatatgccacca-tgcccatcaatctcatgacaatattctttttcattcttctgcagATAAATTCAGATCTGATCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGC

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AC191412.3_FGT002 (Zea mays), 3'ss of exon 1
ctaaccatgttggtcatgatatattatgtaatacttttccatctaata-tttttccttaaattattatatatctcatgaataatttttctggttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC----------
            |       |||  |  | |||  || |||  |||   | |||  |||  | |   || | | |     |||  | |   ||   | |||| |||||||     ||  | ||||| ||||| ||||||||  | ||||||||||||||||||||||| || ||  | |||||  |||| ||||| || ||          
----------ctgaaggaccatagca-atgataaattaccagttaacggtgttttattagttcaaagtaaagcactgatttaacatgtacagtatgttcagataagttcagAGCTGATCTCATGAACATTGCTATGACTACCCTTAGTTCAAAAATTCTTTCCCAGGATAAAGAGTACTTTGCTGAACTTGCAGTTGACGCTGTATTAAGG

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G370693_T01 (Zea mays), 3'ss of exon 2
ctaaccatgttggtcatgatatattatgtaatacttttccatctaatatttttccttaaattattatatatctcatgaataatttttctggttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC
                                                                  || | | |     |||  | |   |||  | |||| |||||||     ||  | ||||| ||||| ||||||||  | ||||||||||||||||||||||| || ||  | |||||  |||| ||||| || ||
-----------------------------------------------------------------gtaaagcactgatttaacatgtacagtttgttcagATAAGTTCAGAGCTGATCTCATGAACATTGCTATGACTACCCTTAGTTCAAAAATTCTTTCCCAGGATAAAGAGTACTTTGCTGAACTTGCAGTTGACGC

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 7
-------------ctaaccatgttggtcatgatatattatg-taatacttttccatctaatatttttccttaaattattata-----tatctcatgaataatttttctggttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC
              |  || | | | |    |||| | | | |  ||   ||   |||   |  |||   |  ||| ||||      ||| | ||  || | ||| ||      | |||| || |||| || ||||||  |||| |||||||||||||||||||| || || ||||| || ||||||||||| |||||||||||| | || || |||||
gtattgttgtttcatccccctttggataggaatatttcagggttgtatcattgtctctgtaaccttttaattcattgttattactattatttaatacattaatttactttaatgtccagAGAAATTCAGGTCAGACTTATTGAACATTGCAATGACTACTTTGAGCTCCAAGATTCTCTCACAGGACAAGGAGCATTTTGCAAAATTAGCTGTGGATGC

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 7
-------------ctaaccatgttggtcatgatatattatgtaatacttttccatctaata-tttttccttaaattattata-----tatctcatgaataatttttctggttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC
                 || | ||||  | |   | ||  |   |   |     |    ||   |||   || |||  |||      ||| | ||  || | |||  |   |  | |||| || |||| || ||||||  |||| |||||||||||||||||||| || || ||||| || ||||||||||| |||||||||||| | || || |||||
gtattgttgtttctccccccttttggatacggatttttcagggttgtatcattgttctgtaaccttttaatacattgctattactattatttaatacattaatttattttattgtccagAGAAATTCAGGTCAGACTTATTGAACATTGCAATGACTACTTTGAGCTCCAAGATTCTCTCACAGGACAAGGATCATTTTGCAAAATTAGCTGTGGATGC

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------------------------------------------ctaaccatgttggtcat--gatatattatgtaatacttttccatctaatatttttccttaaattattatat-atctcatgaataatttttctggttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC
                                                                     | |  |  | |    |  | |  |    || ||    || ||  | |        |  |||| |   | | || | |        | || | || |||||||| ||||| | || ||||||| |||||||||| |||||||||||  |||| |||||||| || ||||||||||||||||||||| || |||| || |||||
gtaatcattatagagatggttaaaccttgttatgctgacatatttaagtatagcattttcttgtttgtgtgattacttcgactgttgggttcaagcggtgatttcctttcagttgaatacagaacggaaatcacactgttattttacagcattgtatttttgtcaatgcagAGAAGTTTAGGTCAGACTTGTTGAAGATTGCGATGACTACTTTATGTTCCAAAATTCTCTCACAGGACAAGGAACATTTTGCAGAAATGGCCGTGGATGC

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ28920 (Selaginella moellendorffii), 3'ss of exon 6
ctaaccatgttggtcatgatatattatgtaatacttttccatctaatatttttccttaaattattatatatctcatgaataatttttctggttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC
                                         |||  |     | ||| |||  ||| |  ||     | |  | | | ||   | ||||||||||||      |||  | || || ||||| ||||| ||| ||||||||||||||||||| ||||| || ||||||||||| || || || ||  ||||
----------------------------------------gtctgttggcactgcttcaatgtttagagctc-----agtcttgtgtttgtccattgcagAAAAGTTTCGACAAGATCTTATCAATATTGCTATGACAACTCTGAGTTCAAAAATTCTTTCTCAGGAGAAAGAACATTTTGCCAATCTTGCTGTGAATGC

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ13624 (Selaginella moellendorffii), 3'ss of exon 6
ctaaccatgttggtcatgatatattatgtaatacttttccatctaatatttttccttaaattattatatatctcatgaataatttttctggttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC
                                         |||  |     | ||| |||| ||| |  ||     | |  | | | ||   | ||||||||||||      |||  | || || ||||| ||||| ||| | ||||||||||||||||| ||||| || ||||||||||| || || || ||  ||||
----------------------------------------gtctgttggcactgcttcaatttttagagctc-----agtcttgtgtttgtccattgcagAAAAGTTTCGACAAGATCTTATCAATATTGCTATGACAACTCTAAGTTCAAAAATTCTTTCTCAGGAGAAAGAACATTTTGCCAATCTTGCTGTGAATGC

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|352769329|gb|FQ471478.1|FQ471478
EST:     TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAG                         AAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAA
genomic: TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAGgtatgcatcc ... gttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAA
EST: gi|71880141|gb|DT029196.1|DT029196
EST:     TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAG                         AAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAA
genomic: TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAGgtatgcatcc ... gttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAA
EST: gi|352782455|gb|FQ470358.1|FQ470358
EST:     TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAA                         AAAAGTTCAAGTTAGACTTGATGA
genomic: TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAGgtatgcatcc ... gttaatgcagAAAAGTTCAAGTTAGACTTGATGA
EST: gi|161714038|gb|FC064113.1|FC064113
EST:     TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAG                         AAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAA
genomic: TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAGgtatgcatcc ... gttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAA
EST: gi|352765070|gb|FQ473718.1|FQ473718
EST:     TGCTCGGAATGCTTTGTTACANAAAGTCATGGATAATAAAGAGGATGCAG                         AAAAGTTCAAGTTAGACCTGATGAAGATTGCAATGACTACTTTGAGT
genomic: TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAGgtatgcatcc ... gttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGT
EST: gi|352773730|gb|FQ472512.1|FQ472512
EST:     TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAG                         AAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAA
genomic: TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAGgtatgcatcc ... gttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAA
EST: gi|352777695|gb|FQ466748.1|FQ466748
EST:     TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAG                         AAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAA
genomic: TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAGgtatgcatcc ... gttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAA
EST: gi|352781730|gb|FQ469028.1|FQ469028
EST:     TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAG                         AANAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAA
genomic: TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAGgtatgcatcc ... gttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAA
EST: gi|352777783|gb|FQ466836.1|FQ466836
EST:     TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAAAAAAGAGGATGCAG                         AAAAGTTCAAGTTAGACTTGATTGA-GATTGCAATGACTACCTTGAGTTCA
genomic: TGCTCGGAATGCTTTGTTACAGAAAGTCATGGATAATAAAGAGGATGCAGgtatgcatcc ... gttaatgcagAAAAGTTCAAGTTAGACTTGAT-GAAGATTGCAATGACTACTTTGAGTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttttccttaaattattatatatctcatgaataatttttctggttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC
     tttccttaaattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaaccatgttggtcatgatatattatgtaatacttttccatctaatatttttccttaaattattatatatctcatgaataatttttctggttaatgcagAAAAGTTCAAGTTAGACTTGATGAAGATTGCAATGACTACTTTGAGTTCAAAAATTCTTTCCCAGGACAAGGAACATTTTGCAAAACTGGCAGTAGATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - ccatgtt
- - - - - -ggtcatg
- - - - - - - - - - - - - - - - - - - ccatcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcatga