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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttaatattactgttgtaaaaattttgtattttcttgtttataatttttctgacagtttgaattcttataatatgataaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAAT

Basic information

species Vitis vinifera
transcript Vv18s0001g14500.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G110574_T01 (Zea mays), 3'ss of exon 8
gttagttaatattactgttgtaaaaattttgtattttcttgtttataatttttctga--cag-tttgaattcttataatatgataaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAAT
    ||  || | | ||||| | |  | || | ||||||  |    ||   ||  ||  |||   | ||  | | |  | |      ||||||||||| || ||||| || ||||||||||| || ||||| ||||| ||||| |||||||| ||||| ||| | || |||||| | ||||| || || ||||
----gtagatttcaatgttg-agagctgtttttttttctgttgggcaacgctttagaatcagacctcaaggcatctggtctatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAAT

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 4
gttagttaatattactgttgtaaaaa---ttttgtattttcttgt-ttataatttttctgacagtttgaattcttataatatgataaa-----atgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAAT
      |||| | | ||| |  | |    |||| | || ||| |  | |||  ||   | | | || |  ||  |   || ||||| |     ||||||||||| || ||||| || ||||||||||| || ||||| ||||| ||||| |||||||| ||||| ||| | || || ||| | ||||| || || || |
-----gtaatttcaatgtcgagagaccatttttcttttgtctggcatcatatcttgctttagacttgggcttgatggcatctgatatatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGT

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 4
gttagttaatattactgttgtaaaaattttgtattttcttgtttataatttttctga--cag-tttgaattcttataatatgataaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAAT
    ||  || | | ||||| | |  | || | ||||||  |    |||  ||  ||  |||   | ||  | |  ||| |      ||||||||||| || ||||| || ||||||||||| || ||||| ||||| ||||| |||||||| ||||| ||| | || |||||| | ||||| || || ||||
----gtagatttcaatgttg-agagctgtttttttttctgttgggcaatgctttagaatcagacctcaaggcatcaaatctatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAAT

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G022909_T01 (Zea mays), 3'ss of exon 5
gttagttaatattactgttgtaaaaattttgtattttcttgtttataatttttctgacag-tttgaattcttataatatgataaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAAT
    ||  || | | |||||  | |  | | | |||| |||   |    |||     |||   | ||  | | |  | |      ||||||||||| || ||||| || ||||||||||| || ||||| ||||| ||||| |||||||| ||||| ||| | || |||||| | ||||| || || ||||
----gtagatttcaatgttg--agagctgttttttttgttgggcaacgctttagaatcagacctcaaggcatctggtctatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAAT

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G063988_T02 (Zea mays), 3'ss of exon 11
gttagttaatattactgttgtaaaaattttgtattttcttgtttataatttttctgacag-tttgaattcttataatatgataaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAAT
    ||  || | | ||||   |    ||| | || | |||   |    |||     |||   | ||  | | |  | |      ||||||||||| || ||||| || ||||||||||| || ||| | ||||| ||||| |||||||| ||||| ||| | || |||||| | ||||| || || ||||
----gtagatttcaatgttcagagctgttttttttctgttgggcaacgctttagaatcagacctcaaggcatctggtctatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTTGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAAT

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 4
-------gttagttaatatta-ctgttgtaaaaattttgtattttcttgtttataatttttctgacagtttgaattc---ttataatatgataa-aatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAAT
        ||  | |||  |   | || | || |   | ||     | |       |  || |     |||| |       || || ||| |     | |||||||| || ||||||||||||||||| || |||||||| || |||||||| |||||||| ||||| ||||| || ||||| || || ||||| |||||| 
ggttagtattgctaaattctggttattatgaagacagtctaaacaat-gccggcggtgctt-tattgttttgcaactaaactaaaacatgctggtgctacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAA-

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 4
------------------------------------------------gttagttaatattactgttgtaaaaattttgta---ttttcttgtttataatttttctgacagtttgaattcttataatatgataaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAAT
                                                 || |   |||| | | || | || |   | ||     | || || | | ||| || ||  |   | || |   | |   || |    | |||||||| || ||||||||||||||||| || |||||||| || |||||||| |||||||| ||||| ||||| || ||||| || || ||||| || ||||
gttagtattgctatattctgattattatgcttttttttttaaggttgtttttggctatatgatttttatgaatacagtctaagcaatgctggtgttttattgttttggaa--ctaaacttaaacatgttggtgc--tacagATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATCGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCGAAAT

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|110723753|gb|EE101423.1|EE101423
EST:     CAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG                         ATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA
genomic: CAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAGgttagttaat ... taaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA
EST: gi|30297571|gb|CB974365.1|CB974365
EST:     TAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG                         ATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA
genomic: TAGGTGAAGGTGATACTGCAAAGCTTGATATCCAGgttagttaat ... taaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA
EST: gi|110710305|gb|EE086522.1|EE086522
EST:     CAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG                         ATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA
genomic: CAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAGgttagttaat ... taaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA
EST: gi|352764021|gb|FQ467591.1|FQ467591
EST:     CAGATGAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTAGGTATCCAG                         ATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA
genomic: CAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAGgttagttaat ... taaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA
EST: gi|110709700|gb|EE085391.1|EE085391
EST:     CAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG                         ATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA
genomic: CAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAGgttagttaat ... taaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA
EST: gi|110726118|gb|EE101621.1|EE101621
EST:     CAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG                         ATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA
genomic: CAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAGgttagttaat ... taaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA
EST: gi|110724805|gb|EE100952.1|EE100952
EST:     CAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG                         ATTANATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA
genomic: CAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAGgttagttaat ... taaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgtttataatttttctgacagtttgaattcttataatatgataaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAAT
                ttctgac  putative branch site (score: 2)
                       agtttgaattcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttaatattactgttgtaaaaattttgtattttcttgtttataatttttctgacagtttgaattcttataatatgataaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC