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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggtttactagagatactgactccctgctttttgataaatgatttgtgagtgcaatatcaattattaatgttttctcatgataacaattttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA

Basic information

species Vitis vinifera
transcript Vv01s0026g01620.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 3
atggtttactagagata--ctgactccctgctttttg-ataaatgatttgtga-gtgcaatatcaattattaatgttttctcatgataacaattttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA
  | |    || |  |   |  |||   |  |||  | |||| |   || ||| |||   | |   |   | || |||      |||||   | ||| |   |||| |  | ||||| ||||||||||| || |||| ||| ||||| |||||||||||||| ||||| ||||||||||| ||||| |||||||||||||| ||
--gttgcgttaaatttggcccaactgtttcatttcagtataactctattctgaagtgtcttgtatttatctgatatttgtcttggataattgtattaaac--agGGTCTTTACCTCTCCCATGGGCCATCAGAATGAGAATAGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTA

upper sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------------------------------------------------atggtttactagagatactgactccctgctttttga---taaatgatttgtgagtgcaatatcaattattaatgttttctcatgataacaattttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA
                                                                                            | | |     ||  |  |   ||  ||| | |||    |  |  |  | | |     |||  |||  | ||| || |   |||||      || |  | ||||| | || ||||| || ||| |||| || |||||  |||| || || || || ||||||||||| || |||||||| ||||||||||| |||||||| ||
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttat---atgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA

upper sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
-atggtttactagagatactgactccctgctttttgataaatgatttgtgagtgcaatatcaattatta-atgttt-tctcatgataacaattttatat---gtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA
     ||||   |  | | |    |  || | |||      || ||||| |   ||   | ||   | | ||     ||| || | |    |||| |||    ||| | |  ||||||| ||||||||||| || ||||||||||| || |||||||| || || || || ||||||||||| ||||| ||||| ||||| || ||
aggattttatgtgctaaatttgaccagtgttgttt------tgttttgtcataacatcttgaaccttcacatacccatctaataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA

upper sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------------------atggtttactagag---atactgactccctgctttttgataaatgatttgtgagtgcaatatcaattatta-----atgtt---ttctcatgataacaattttatat------gtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA
                                                                                   |    ||  || |   ||  ||    ||||  |||   |   |   ||  |  | |  ||   | ||| |     |||||   |  | | |  ||||||| |   |      |||||| | || ||||| |||||||| || || |||||  ||||||| || || || |||||||| || || |||||||| ||||||||||| ||||| || ||
gtatgtatctggcttattccttaatgattggagcactaacttctgtttaggattcacctttttttcttaagcaaataatcgtgtatcatatgagggcgcatgatgttctcctgtatttatttgtgtagcttaggcatcctttaaatagtatcatggaaatgttgaatcttaaagtaaacaattctgctttctactgtagGGTCTCTTCCTCTCCCATGGGCTATCAGAATGAAGGTTGCACTGGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGTCCAGTCATTTA

upper sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------------------------------------atggtttactagagatactgactccctgctttttgataaatgatttgtgagtgcaatatcaattattaatgtttt-ctcatgataacaattttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA
                                                                                                    || |||     |  ||| | | |        || ||       |   | |||   ||   |||  | ||| ||   |  || ||     |||    ||||||| | || ||||| |||||||| || || |||||  ||||||| || || || |||||||| || || |||||||| ||||||||||| ||||| || ||
gtatgtatctagcttattccttagcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggctttgaat-agtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA

upper sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 3
atggttt-actagagatactgactccctgctttttgataaatgatttgtgagtgcaatatcaattattaatgttttctcatgata-acaattttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA
 ||| |  | ||  |||    ||| |   ||| |   || |   |||||       ||||| ||| |  ||||| ||   | | | |  || |  | ||||||| ||||||||||||||||| |||| ||||||||||||||||| || ||||| ||||||||||| ||||||||||||||||| ||| | ||||| |||||
gtggatggattatggattggaacttcaaacttctgcttatactctttgttttgattatatccattgt--atgttctcatgtaaaagattatatgttttgtagGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATA

upper sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 4
atggtttactagagatactgactccctgctttttgataaatgatttgtgagtgcaatatcaattattaatgttttctcatgataacaattttatatgt-----agGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA
 ||    |  |  |||    ||| |   ||| |   || |   |||||       ||||| ||| |     | ||||||||   | |||| |||||||     |||| |||| |||||||||||| |||| |||||||||||||||||||| ||||| ||||||||||| |||||||| |||||||| ||| | ||||| |||||
-tgaaagagaatggattggaacttcaaacttctgcttatactctttgttgtgattatatccattgt----atgttctcatgtacaaaattatatatgttttgtagGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATA

upper sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 3
-------atggtttactagagatactgactccctgctttttgataaatgatttgtgagtgcaatatcaattattaatgttttctcatgataacaattttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA
        ||||  |  |   |  |  |     |||| | |  |      |||| || |      |   ||||| ||||| ||   ||  ||  |      |||||||  || |||||||||||||| |||| || ||||||||||||||||| ||||||||||||||||| ||||||||||| ||||| ||| | ||||| |||||
tctatcattggtagaacaagaactcaaaactattgctgtatatttttatgtttg-gattttgtccttttttatttatgttctcatgtggaaatta------atgtagGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA

upper sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G02570.1 (Glycine max), 3'ss of exon 3
-atggtttactagagatactgactccctgctttttgataaatgatttgtgagtgcaa--tatcaattattaat-gttttctcatgataacaattttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA
     | |     |||    ||   |     | ||| |  ||  ||| ||  || |   | ||  || ||| |  | |||||||| |   ||||    |||||||  || | |||||||||||| |||| || ||||||||||||||||| ||||||||||||||||| ||||||||||| ||||| ||| | ||||| |||||
ctctatcttgggtagaactggaactcaaaactattgctgtatattttatgtttgtattttgtccctttttatttatgttctcatg-tggaaatta---atgtagGATCCATTCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA

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|161715633|gb|FC066791.1|FC066791
EST:     AGTTTATGAGTTTATGCCTCGAGGAAGTTTGGAGAATCATCTGTTTAGGA                         GGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTG
genomic: AGTTTATGAGTTTATGCCTCGAGGGAGTTTGGAGAATCATCTGTTTAGGAgtatgtacct ... ttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgagtgcaatatcaattattaatgttttctcatgataacaattttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA
                                  tgataac  putative branch site (score: 2)
               aattattaatgttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggtttactagagatactgactccctgctttttgataaatgatttgtgagtgcaatatcaattattaatgttttctcatgataacaattttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA

- - - - - - - -tactgac
- - - - - - - - - - - -ccctgct
- - - - - - - - - - - - - - - - - - - - - - - -tgagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataacaa