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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttaaaattgtttcagtggatttacttgtttgcagcttcttgtgttttgcactttaatgttgttgcttttgcatgatttttatatcggctcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAAAACTTGCCTTATCTTAATCGGTTGGGTACTTTGCTTATCAACAACAATA

Basic information

species Vitis vinifera
transcript Vv01s0150g00590.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g13990.3 (Oryza sativa), 3'ss of exon 2
---ctttaaaattgtttcagtggatttacttgtttgcagcttcttgtgttttgcactttaatgttgttgcttttgcatgatttttatatcggctcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAAAACTTGCCTTATCTTAATCGGTTGGGTACTTTGCTTATCAACAACAATA
     | |   |  |||||||   |   |  | ||     || || | || |   ||  |   |  ||     | | |  ||| |   |  ||||      ||||||||||||| || ||||| ||||| |||||||||||||||||||| || ||||| || ||  | |||||  | || ||| || |  | ||||| || |
aatactcattctcatttcagtatttgacccagcttttgttttattatcttcttt-ctccagcatgtttaacacttctt--tttgttactttgctctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAGAACTTCCCGTACTTGAATCGTCTTGGCACTCTGTTAGTTAACAATAACA

upper sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G021742_T01 (Zea mays), 3'ss of exon 2
-ctttaaaattgtttcagtggattta--cttgtttgcagcttcttgtgttttgcactttaatgttgttgcttttgcatgatttttat--atcggctcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAAAACTTGCCTTATCTTAATCGGTTGGGTACTTTGCTTATCAACAACAATA
   |   || | ||  |    |||||   | || |  || |  ||| |||     || ||   ||      ||  ||  || | |||  |    |||  |  |||||||| ||||| || ||||| ||||| || ||||||||||||||||| |||||||| || ||  | |||||  | || ||| | ||  | || || || |
gaatagtaaattttaaatcttatttagaatggtatttagttgtttgggttcctt-ctctagcctt----tcttaacaccatctatattcactctctctctaacagGACCAGTTTGACACAATTGACTTGTCGGATAATGAGATTGTCAAGCTTGAAAACTTCCCATACTTGAATCGTCTTGGCACTCTACTAGTTAATAATAACA

upper sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G24350.2 (Glycine max), 3'ss of exon 3
--------------------------------------ctttaaaattgtttcagtggatttacttgtttgcagcttcttgtgttttgcacttt----aatgttgttgcttttg--catgatttttatatcggctcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAAAACTTGCCTTATCTTAATCGGTTGGGTACTTTGCTTATCAACAACAATA
                                      | ||| | |||      |  ||     ||  |    |||| | |||  | || ||     ||  ||  | ||| ||  | | | |||   || |  |     |||||||||||| || || || || || |||||||||||||||||||| || |||||  | || |||||||| |||||||||||  |||| || |||||||| |
gtgcacaatttaatcttcttcccttccttttagtttccccttatatttgaaaggatatatcgttatgactctgtcttcatatgtgcttcatttataaaaaaattcatccttgtgttcttaaatttgcaatggattttcctgcagGACCAATTCGACACAATAGACTTATCTGACAATGAGATTGTCAAACTTGAAAATGTACCATATCTTAACCGGTTGGGTACAATGCTCATTAACAACAACA

upper sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G18440.2 (Glycine max), 3'ss of exon 3
-----------------------------------------ctttaaaat-tgtttcagtggatttacttgtttgcagcttcttgtgttttgcactttaatgttgttgcttttgcatgatttttatatcggctcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAAAACTTGCCTTATCTTAATCGGTTGGGTACTTTGCTTATCAACAACAATA
                                          || ||| | | | | | |    ||   | |||  |  | |||   || |  |      |  |  || | || ||| | |||   || |  |     ||||||||||||||| || || || || ||||||||||||||||| || || |||||  | || |||||||| |||||||| ||  |||| || |||||||| |
gtgcaaaatttaatcttccttcctttcagtttccccttatatttgaaagtatatattattatgattctctctttatatatgcttcaattataaaaaaacttcatcctggtgtt-cataaatttgcaatggattttcctgcagGACCAATTTGACACAATAGACTTATCTGACAATGAGATTGTTAAACTTGAAAATGTACCATATCTTAACCGGTTGGGCACAATGCTCATTAACAACAACA

upper sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G09760.1 (Arabidopsis thaliana), 3'ss of exon 2
----ctttaaaattg--tttcagtggatttacttgtttgcagcttcttgtgttttgcactttaatgttgttgcttttgcatgatttttatatcggctcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAAAACTTGCCTTATCTTAATCGGTTGGGTACTTTGCTTATCAACAACAATA
    || ||| |  |   | |  |  ||||   ||||||      |||  ||     | ||  | |||   | || |  |      || | | || |   |  |||||||| || |||||||||||| ||||||| || ||||| || ||||| |||||||| || || || || || || || ||||| || ||||| |||||| 
tcttctctaagaaaggcctcccataaattt-tgtgtttgg-----cttaggtagattatttgcaggtttgaggttctctaattaacttgtcttggtttgcttacagGACCAGTTCGATACCATTGATCTGTCTGATAACGAGATAGTTAAGCTAGAAAACTTCCCATACCTCAACCGTTTAGGAACTTTACTCATCAATAACAATC

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|110712685|gb|EE087945.1|EE087945
EST:     GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAG                         GACCAATTTGATACCATTGATTTGTCCGACAATGAGATTGTCAAGCTCGAA
genomic: GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAGgtgtgtttgc ... tcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAA
EST: gi|110429737|gb|EC996240.1|EC996240
EST:     GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAG                         GACCAATTTGATACCATTGATTTGTCCGACAATGAGATTGTCAAGCTCGAA
genomic: GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAGgtgtgtttgc ... tcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAA
EST: gi|110710820|gb|EE087309.1|EE087309
EST:     GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAG                         GACCAATTTGATACCATTGATTTGTCCGACAATGAGATTGTCAAGCTCGAA
genomic: GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAGgtgtgtttgc ... tcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAA
EST: gi|32269037|gb|CD718196.1|CD718196
EST:     GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAG                         GACCAATTTGATACCATTGATTTGTCCGACAATGAGATTGTCAAGCTCGAA
genomic: GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAGgtgtgtttgc ... tcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAA
EST: gi|161708201|gb|FC057845.1|FC057845
EST:     GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAG                         GACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAA
genomic: GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAGgtgtgtttgc ... tcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAA
EST: gi|110701540|gb|EE079224.1|EE079224
EST:     GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAG                         GACCAATTTGATACCATTGATTTGTCCGACAATGAGATTGTCAAGCTCGAA
genomic: GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAGgtgtgtttgc ... tcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAA
EST: gi|161714413|gb|FC064424.1|FC064424
EST:     GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAG                         GACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAA
genomic: GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAGgtgtgtttgc ... tcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAA
EST: gi|110702872|gb|EE079225.1|EE079225
EST:     GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAG                         GACCAATTTGATACCATTGATTTGTCCGACAATGAGATTGTCAAGCTCGAA
genomic: GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAGgtgtgtttgc ... tcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAA
EST: gi|161708757|gb|FC060880.1|FC060880
EST:     GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAG                         GACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAA
genomic: GGAATAAGGTTGCTGTAATTGAGAACTTGGGCGCTACAGAGgtgtgtttgc ... tcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcactttaatgttgttgcttttgcatgatttttatatcggctcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAAAACTTGCCTTATCTTAATCGGTTGGGTACTTTGCTTATCAACAACAATA
       ctttaat  putative branch site (score: 4)
                            atgatttttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttaaaattgtttcagtggatttacttgtttgcagcttcttgtgttttgcactttaatgttgttgcttttgcatgatttttatatcggctcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAAAACTTGCCTTATCTTAATCGGTTGGGTACTTTGCTTATCAACAACAATA

- - aaaattg
- - - - - - - - - - - - - - - - -cagcttc
- - - - - - - - - - - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgat