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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatctggattttctgttggcaacttgttaactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC

Basic information

species Vitis vinifera
transcript Vv09s0002g04810.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 6
gtatgatctggattttctgttggcaacttgttaactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
    | |   |||||| |       | ||| |      | |||||  |   | |  | |      || ||  | ||    |  ||| ||     ||| |  |||  ||| |||||| |||||| || || || |||||||| ||| | |||| ||||   ||||| || |||||||||||||||||||| || ||||||   |||||  
----gtttgcgattttgttccttacatttgcttggcatagttttt-gcatttctaacatttcttggtctggatttgaatgtggtgccct-----tatttaattt--cagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 6
gtatgatctggattttctgttggcaa-cttgttaactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttc---------cagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
|| ||   |   |   || |    |  || |||  |  || | ||  |  | ||| |   |  || |    ||  |  |  |       || |||||||   ||||          |||||||||| |||||| ||||| ||||| ||||| ||||| |||| ||||   ||||| || || |||||||||||||| || || ||||||  |||||| |
gtttgtgttatctccgctttaaaaattctggttggccacaatgttgcatta-tttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 6
gtatgatc-tggattttctgttggcaacttgttaactgcatttttttaccaattttgcttcatcaagtatgagtgtgctattta-tgctctgatga------tatc-tccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
|| | ||  ||   ||  |  |||    || ||   |  |       |  ||  |      |  || |||||   |   || || |||  |||||       |||| ||  ||| ||||| ||||||||||||||||| ||||||||||||||  ||||||| ||||||||||| || |||||||||||||| |||||||| ||||| ||||||||||
gtgtaattatgttcttgttcctggatgtttcttttttaaaaaaaaaaa--aaagtaaaaagaaaaactatgatcctatgatataatgcattgatgcaactgttatcatctcttttcagATTTGGAATCTTGGCTCTCCTGACCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 6
gtatgatctggattttctgttggcaacttgtt-aactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
                             ||  || |   || || | ||   || | ||| |    ||| |   ||| ||| |||| |   |  | |   |||||| |||| ||||||||||||||||| || |||||||||||  ||||||| ||||||||||| || |||||||||||||| |||||||| ||||| ||||||||||
-----------------------------gtagaattatgttcttgttcctggtt-gtttcctatgatataa---tgc-attaatgcacctgttgtcttctcttttc-agATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
gtatgatctggattttctgttggcaacttgttaactgcatttt-tttaccaattttgcttcatcaa--gtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
|||| ||     | ||||  | || | ||||   ||| ||||| |||    ||||   | |||| |   ||  | | |   | | |||   | ||| ||||| |  || ||||| ||||||||||||||||| ||||| ||||||||  ||||||||||||| ||||| || ||||||||||||||||||||||| ||||| ||||| || |
gtat-atacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 6
gtatgatctggattttctgttggcaacttgttaactgcatttt-tttaccaattttgcttcatcaa--gtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
     ||     | ||||  | || | ||||   ||||||||| |||    ||||     || | |   ||  | |     | | |||   | ||| |||||  | || ||||| ||||||||||||||||| ||||| ||||||||| ||||||| ||||| ||||| || ||||||||||||||||||||||| ||||| || || ||||
---gtatacatgtgttcttcttgctagttgtgtcctgcattttctttgtttatttccaaacacctatgataaaaattaaaaagtaatgtattaatgttatcttttcttgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACATTGGATGCGCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAGCCTTATC

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 6
gtatgatctggattttctgttggcaacttgttaactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
   ||     ||  | |        |  | |||  ||  ||  ||  |      | |||    |||  |   | |  ||       | | ||| | | | | | | ||||||||||||||||| || |||||||| ||||||||||||||||| ||||||||||| || || ||||| ||||| || ||||| ||||||||||| ||||
--gtgtgtaagaggtccaagcactgagctttta--tggcttagttagcacgaggtacttttaaaagggt---tttcttagactaattttcatgct-tgttcatattcagATATGGAATCTTGGTTCCCCAGACCCAAATTTTACACTGGATGCTCATCAGAAAGGAGTCAACTGTGTAGATTATTTCACAGGGGGTGATAAACCCTATC

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgatctggattttctgttggcaacttgttaactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
                 || ||  || | ||  |   ||||     | || | | | ||  ||   |  |   |  |  | || | |   |||  || | | | | ||||| ||||||||||| || |||||||| ||||||||| ||||||||||||||||||| ||||||||||| ||||| || || || |||||||| || ||| 
----------------gtgctg--aaatggtcta--acattgaaacatcattatggtttagtccgcttagtccgctcattctacgtttacatg-catgttcatcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatgatctggattttctgttggcaacttgttaactgcattttt--ttaccaattttgcttcatca--agtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
||| |||  |  | |||   |   || ||   | || | | |||  || |||||||  | | || |  ||  | |   |  | ||  ||     |  || | | |||  | |||||||||||||||||||||| || || ||||||||  ||||||| ||||  ||||||||||| ||||| || |||||||| || || ||||||||||| |
gtaagattag--tcttcaacttttaagttac-accttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctac-atcttttcttacctagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTGGATGCACATCTCAAAGGGGTAAACTGTGTAGACTACTTTACTGGTGGGGATAAACCATACC

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|110386870|gb|EC951502.1|EC951502
EST:     CAAAAGATACCAACACTTTTGCTAGTGCATCTCTGGATCGCACCATTAAG                         ATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAG
genomic: CAAAAGATACCAACACTTTTGCTAGTGCATCTCTGGATCGCACCATTAAGgtatgatctg ... ccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAG
EST: gi|110388767|gb|EC953553.1|EC953553
EST:     CAAAAGATACCAACACTTTTGCTAGTGCATCTCTGGATCGCACCATTAAG                         ATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAG
genomic: CAAAAGATACCAACACTTTTGCTAGTGCATCTCTGGATCGCACCATTAAGgtatgatctg ... ccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
                               ctctgat  putative branch site (score: 4)
                                        tatctccttttcc  putative PPT
                       tatttat  TA-rich tract