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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCAGAAGCTCTTAGGCTGGTCTTAACTCAAGTCCTTCTCCAAAAGAAGGGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatctgatgctttattaaccctattttttaagtatgtctccccgctcaatttatggctagctgagtaaaagaagaaaaaatcaactgttcttga...

Basic information

species Vitis vinifera
transcript Vv05s0020g00740.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00740.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os03g49570.1 (Oryza sativa), 5'ss of exon 6
TTGCAGAAGCTCTTAGGCTGGTCTTAACTCAAGTCCTTCTCCAAAAGAAGGGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatctgatgctttattaaccctattttttaagtatgtctccccgctcaatttatggctagctgagtaaaagaagaaaaaatcaactgttcttga----
|||| ||||| || ||||||||  | || || ||||| || ||||||||||| || |||||||| |||||||| ||||||||||| || || || ||||||||    | || ||   | |  ||   |  ||  |   ||||  | |     ||| |   |   |    | |||            | || | ||   ||    
TTGCGGAAGCCCTCAGGCTGGTTCTGACACAGGTCCTCCTTCAAAAGAAGGGGTTAACTCTAAACCCTATCACAAGCCTATATTATATAGCCCCTTGCAGgtattgcaact-atatctgaa-aagtttgcttgcttgatatgatttc--aaccaactaccgttgaatgaaataacgacttctctcttaaagtcttacagaatac

upper sequence: Vv05s0020g00740.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G002699_T01 (Zea mays), 5'ss of exon 4
TTGCAGAAGCTCTTAGGCTGGTCTTAACTCAAGTCCTTCTCCAAAAGAAGGGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatctgatgctttattaacccta---ttttttaagtatgtctccccgctcaatttatggctagctgagtaaaagaagaaaaaatcaactgttcttga
|||| ||||| || ||||||||| ||||||| ||||||||||||||||||||||| || || ||||| || || ||| | |||||||| || || ||||||||| | |     |  | |   |  |  |    | | | | |   | |       |     | | |    | |  | |     |    || |  | || ||| 
TTGCGGAAGCCCTCAGGCTGGTCCTAACTCAGGTCCTTCTCCAAAAGAAGGGCTTAACCCTGAATCCCATTACAAGCTTGTATTACATAGCCCCTTGCAGgtactagaaactgtattctgacattctaaaggctctcttaattgatataattttcccgacaaggaccgtttaatgacattgctatgttatga--tatttttg-

upper sequence: Vv05s0020g00740.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA15G21500.1 (Glycine max), 5'ss of exon 6
TTGCAGAAGCTCTTAGGCTGGTCTTAACTCAAGTCCTTCTCCAAAAGAAGGGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatctgatgctttattaaccctattttttaag-tatgtctcc-----ccgctcaatttatg-gctagctgagtaaaagaagaaaaaatcaactgttcttga
||||||||||| | || ||||||||||| ||||| ||||| || || ||||| ||||||||||||||||| || ||| |||||||||| ||||||||||||||       ||||  | | | |    | || |  ||| ||  || |      | |  ||||||     |   ||||    ||  ||||||  |   | |||     
TTGCAGAAGCTTTAAGACTGGTCTTAACGCAAGTTCTTCTGCAGAAAAAGGGGTTGACTCTAAATCCTATTACAAGCTTATATTACATAGCTCCATGCAGgtatttctgttgatattct-taagtagttttctcaaagatacatcactggattctgtacaattttcatacatactgaacccaaacagaaaatgt-ggcagtt-----

upper sequence: Vv05s0020g00740.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA13G18040.1 (Glycine max), 5'ss of exon 6
TTGCAGAAGCTCTTAGGCTGGTCTTAACTCAAGTCCTTCTCCAAAAGAAGGGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaat-ctgatgcttt-attaaccctat---tttttaagtatgtctccccgctcaattta-tggctagctgagtaaaagaagaaaaaatcaactgttcttga
|||| |||||| | || ||||||||||| ||||||||| | || ||||||||||||| | |||||||||| || ||| |||||||||| ||||||||||||||     |  ||||| ||| | | |    ||   |   ||| || |||       ||| |  | |||  |  | |    | |  || | | |   || ||     
TTGCTGAAGCTTTAAGACTGGTCTTAACACAAGTCCTTTTACAGAAGAAGGGCTTGAGTTTAAATCCTATTACAAGCTTATATTACATAGCTCCATGCAGgtatattctgttgatgttttcaatgagtaaataaataaataaata-gtcaattgagtcagtgcagtggtcatattaacccacgtcgacagatttctctttt-----

upper sequence: Vv05s0020g00740.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA17G04450.1 (Glycine max), 5'ss of exon 6
TTGCAGAAGCTCTTAGGCTGGTCTTAACTCAAGTCCTTCTCCAAAAGAAGGGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaat-ctgatgctttattaaccctattttttaagtatgtctccccgctcaattta-tggctagctgagtaaaagaagaaaaaatcaactgttcttga---
|||| |||||| | || ||||||||||| ||||||||| | || ||||||||||||| | |||||||||| || ||| |||||||||| ||||||||||||||    ||  ||||| |||   |||   | |   ||| || |||       ||| | || |||  |  | |    |    || | | |   || |||       
TTGCTGAAGCTTTGAGACTGGTCTTAACACAAGTCCTTTTACAGAAGAAGGGCTTGAGTTTAAATCCTATTACAAGCTTATATTACATAGCTCCATGCAGgtatattatgttgatgtttt--caacg--agtaaataaata-gtcaattgagtcagtgtagtggtcatattaacccacatggacagatttctcttttcccactaa

upper sequence: Vv05s0020g00740.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA09G09220.1 (Glycine max), 5'ss of exon 6
TTGCAGAAGCTCTTAGGCTGGTCTTAACTCAAGTCCTTCTCCAAAAGAAGGGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatctgatgctttattaaccctattttttaagtatgtctccccgctcaatttatggctagctgagtaaaagaagaaaaaatcaa-ctgttcttga
||||||||||| | || ||||||||||| ||||| ||||| || || ||||| |||||| |||||||||| || ||| |||||||||| ||||| ||||||||       ||||  | |        | | | | |  ||  || |     ||  |  |   |||     || | | |     ||  ||| | |    || 
TTGCAGAAGCTTTAAGACTGGTCTTAACACAAGTTCTTCTGCAGAAAAAGGGGTTGACTTTAAATCCTATTACAAGCTTATATTACATAGCTCCCTGCAGgtatttctattgatattctcaagtagttttctctaagatacatcactggattctgtacaatactacaattgtcatacatactgaacccaaacagaaaatg-

upper sequence: Vv05s0020g00740.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT1G48230.1 (Arabidopsis thaliana), 5'ss of exon 7
TTGCAGAAGCTCTTAGGCTGGTCTTAACTCAAGTCCTTCTCCAAAAGAAGGGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtac-caaatctgatgctttattaaccctattttttaagtatgtctccccgctcaatttatggctagctgagtaaaagaagaaaaaatcaactgttcttga--
|||| ||||| ||||| |||||  |||||||||| ||||| || || |||||||||||  | || ||  |||||||| |||| || || ||||||||||||||| ||   ||||  |      ||||   ||| |||  ||  | ||  |     ||  ||   |  |  | ||       |     |  |||     |||  
TTGCTGAAGCACTTAGACTGGTGCTAACTCAAGTTCTTCTTCAGAAAAAGGGCTTGACGTTGAACCCAGTCACCAGCTTATACTATATAGCTCCATGCAGgtacgcagtcctgacacagctcaaacc---tttcttatttaaatttcagcttaagatgaatacttgtcctaatacttcgtcagttcgttgacttgatgtgacc

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|351053340|gb|FQ459208.1|FQ459208
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|349820070|gb|FQ404792.1|FQ404792
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|349822247|gb|FQ412511.1|FQ412511
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|349812091|gb|FQ410888.1|FQ410888
EST:     GGCTTGACTCTAAATCCCATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCCGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|351019691|gb|FQ439508.1|FQ439508
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|349808616|gb|FQ405760.1|FQ405760
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|349816192|gb|FQ403688.1|FQ403688
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|349811641|gb|FQ409638.1|FQ409638
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|349819593|gb|FQ413477.1|FQ413477
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|30302576|gb|CB979370.1|CB979370
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|349813009|gb|FQ411249.1|FQ411249
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|351042064|gb|FQ456274.1|FQ456274
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|349816269|gb|FQ399379.1|FQ399379
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|349831143|gb|FQ420813.1|FQ420813
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
EST: gi|351034409|gb|FQ463222.1|FQ463222
EST:     GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAG                         TTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA
genomic: GGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatc ... tcatgtgcagTTTTGTGTTTCTATTTGTACCCTGGTATTTTTTGGAGAAGCCACAGATGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCAGAAGCTCTTAGGCTGGTCTTAACTCAAGTCCTTCTCCAAAAGAAGGGCTTGACTCTAAATCCTATCACCAGCCTATATTACATTGCTCCATGCAGgtaccaaatctgatgctttattaaccctattttttaagtatgtctccccgctcaatttatggctagctgagtaaaagaagaaaaaatcaactgttcttga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat