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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggattttttattttttatttttaatgcaaattcttagcagtatatattcttgattccacttgcagcacatttcagcagcttttggtatttggtgcattttgcagGTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTCATTCTTATGGTATTACAAGGCATCGCCATG

Basic information

species Vitis vinifera
transcript Vv03s0063g01110.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 3'ss of exon 9
gttaggattttttattttttatttttaatgcaa--attcttagcagtata-tattcttgattccacttgcagcacatttcagcagcttttggtatttggtgcattt-tgcagGTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTCATTCTTATGGTATTACAAGGCATCGCCATG
|   | |  ||    |  | |  |    | | |  ||   ||  | | || |  |  |   ||  |    |  ||   |||     | |   || |   ||||||| || ||| ||||| || |||||||| ||||| |||||||| |||||||||||||| ||| ||||||| || | | | || || ||||
gcatgtaacttgagatactgacgtactgtactactatggctacaaatttagtggttgtatatctgccatgattactagtcaatctttctctctaatgcatgcatttgtgtagGACGTGGAGCGAAGGAGGCGAATCTTTACACTGAGATAGCTGAAGGCATCCATGCTTATGGAATAAAAGGCCACCGTCATG

upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 9
--------------------gttaggattttttattttttattttta---atgcaaattcttagcagtatatattcttgattccacttgcagcacatt-tcagcagct--tttggtatttgg----tgcattttgcagGTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTCATTCTTATGGTATTACAAGGCATCGCCATG
                      |  || | || | |  |||| | ||   ||  | ||   ||    |||||||   |   |  |  |  |   |||  | |  ||||  | || | | |      || |||||| ||| ||||| || ||||| || ||||| ||||| || |||||||||||||||||| ||||||| || | | | || || ||||
gtatgcattttgcatgagatactctgactattaagtaattatatatatatatatatatatatatatatatatatatatatatatatatatatgccatcattattagctgatatgctgtgtaacacatgtattttgtagGACGTGGAGCTAAGGAAGCCAATCTCTACACCGAGATAGCTGAAGGCATTCATGCTTATGGAATAAAAGGCCACCGGCATG

upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 9
gttaggattttttattttttatttttaatgcaaattcttagcagtatatattcttgattccacttgcagcacatttcagcagcttttggtatttggtgcattttgcagGTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTCATTCTTATGGTATTACAAGGCATCGCCATG
           ||  | |||||||   ||  ||    ||  || | |||||   || ||| || |  |    ||||     |  | |   |  ||   ||||  | ||| ||||| || ||||| |||||||| ||||||||||| ||||| || || ||| ||||||| || ||||| ||||| ||||
----------gttcgtatttatttgagat-taatcgatt--cattttatatatctgtttcaacatcaaatg-attt----ggtctctaaaacatgcatcatt--gtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG

upper sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT2G19940.1 (Arabidopsis thaliana), 3'ss of exon 9
gttaggattttttattttttatttttaatgcaaattcttagcagtatatattcttgattccacttgcagcacatttcagcagcttttggtatttggtgcattttgcagGTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTCATTCTTATGGTATTACAAGGCATCGCCATG
                      ||| |    |     | | || |  | | |   ||| | |  |        ||  ||   |||     || ||     ||   |||| |||||||| |||||||||||||| ||| |||| |||||||||||||||  |||||||||| | ||  | ||||||||||
---------------------gtttgagcttactccgtgatcaatgaacaat---gatgcaatgt--------ttctagtttcttgactgatatgaaattttcatcagGACGTGGTGCTAAGGAGGCAAATCTTTACTCTGAGATAGCTGAAGGCATTTCTTCTTATGGTGTCACCCGTCATCGCCATG

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|110390116|gb|EC955007.1|EC955007
EST:     TGAAACAAGAAATCTCATTATTGATGCAAAATCTGGTGTGAGTGGAGCAG                         GTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTC
genomic: TGAAACAAGAAATCTCATTATTGATGCAAAATCTGGTGTGAGTGGAGCAGgttaggattt ... cattttgcagGTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTC
EST: gi|110729272|gb|EE105384.1|EE105384
EST:     TGAAACAAGAAATCTCATTATTGATGCAAAATCTGGTGTGAGTGGAGCAG                         GTCNTGGTGCCCAAG-AGGCAAATCTGTACACTGAAATAGCTGAAGGCATT
genomic: TGAAACAAGAAATCTCATTATTGATGCAAAATCTGGTGTGAGTGGAGCAGgttaggattt ... cattttgcagGTCGTGGTGCC-AAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATT
EST: gi|27583381|gb|CB006076.1|CB006076
EST:     TGAAACAAGAAATCTCATTATTGATGCAAAATCTGGTGTGAGTGGAGCAG                         GTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTC
genomic: TGAAACAAGAAATCTCATTATTGATGCAAAATCTGGTGTGAGTGGAGCAGgttaggattt ... cattttgcagGTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattccacttgcagcacatttcagcagcttttggtatttggtgcattttgcagGTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTCATTCTTATGGTATTACAAGGCATCGCCATG
 tcttgat  putative branch site (score: 4)
                                    tattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggattttttattttttatttttaatgcaaattcttagcagtatatattcttgattccacttgcagcacatttcagcagcttttggtatttggtgcattttgcagGTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTCATTCTTATGGTATTACAAGGCATCGCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG