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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgccaccttggtggggtttagccactgatctggttttgagaaacttttggattatttgtgagttttctatgacatagttccttgatgccaattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCTGCCTCTGCAGCTAATGGTACAACTGCTCCTGGTGCCCCACCAAGGCCTT

Basic information

species Vitis vinifera
transcript Vv08s0007g04710.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G00840.1 (Glycine max), 3'ss of exon 5
ctgccaccttgg-tggggtttagccactgatctggttttgagaaacttttggattatttgtgagttttctatgacatagttcc--ttgatgccaattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCTGCCTCTGCAGCTAATGGTACAACTGCTCCTGGTGCCCCACCAAGGCCTT
 |||   ||||  |    | |  |   |  | |||||| |    | |  |   | ||||      | |       ||   |    ||||| |   || | ||| | ||||||||||| ||| ||||||| |||||||| ||||| || |||||||||||| | || ||||| ||| |  |  ||||||  |||||||||||||
-tgctttcttgccttaattctttctgtttgtgtggttt-gcattattgatatttaatttccaccatctgcgatggatgacttgaattgatacttgtt-tgcagCTACAATTGTATTTTAAATCCAAGCCGCCAGAGGCGAACAAACCGCAGCCTGCCTCTACTGCCAATGGCACAGCACCATCTGGTGTACCACCAAGGCCTT

upper sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G44430.1 (Glycine max), 3'ss of exon 5
ctgccaccttgg-tggggtttagccactgatctggttttgagaa--acttttggattatttgtgagttttctatgacatagttccttgatgccaattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCTGCCTCTGCAGCTAATGGTACAACTGCTCCTGGTGCCCCACCAAGGCCTT
 |||   ||||  |    |||  |   | || |||  |  |  |    | ||  ||| |     |  |  |  |||     |   ||||| |   || | ||| ||||||||||||| ||| ||||||| |||||||| ||||| || ||||||||| || | || ||||| ||| |  |  ||||||  |||||||||||||
-tgctttcttgccttaattttttctgtttatgtggcgtgcattattgatatttaatt-tccaccatctgccattgatgacttgaattgatacttgtt-tgcagCTGCAATTGTATTTTAAATCCAAGCCGCCAGAGGCGAACAAACCACAGCCTGCCACTACTGCCAATGGCACAGCGCCATCTGGTGTTCCACCAAGGCCTT
















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|110713132|gb|EE088784.1|EE088784
EST:     CCACTCCAAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACG                         TTGCAATTGTATTTTCAAA-CCAAGCCACCAGAAGCAAACAAGCCTCAGCC
genomic: CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACGgtttgtctgt ... aattgtacagTTGCAATTGTATTT-CAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCC
EST: gi|30134998|gb|CB920336.1|CB920336
EST:     CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACG                         TTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
genomic: CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACGgtttgtctgt ... aattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
EST: gi|110710951|gb|EE087592.1|EE087592
EST:     CCACTCCAAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACG                         TTGCAATTGTATTTCAAAACCAAGCCACCAGAAGCAAACAAGCCTCACCCT
genomic: CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACGgtttgtctgt ... aattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
EST: gi|30133297|gb|CB918636.1|CB918636
EST:     CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCANAAATGTTCACG                         TTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
genomic: CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACGgtttgtctgt ... aattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
EST: gi|110713768|gb|EE089980.1|EE089980
EST:     CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACG                         TTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
genomic: CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACGgtttgtctgt ... aattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
EST: gi|110686098|gb|EE063396.1|EE063396
EST:     CCACTCCAAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACG                         TTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
genomic: CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACGgtttgtctgt ... aattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
EST: gi|156739019|gb|EV243140.1|EV243140
EST:     CCACTCCAAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACG                         TTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
genomic: CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACGgtttgtctgt ... aattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
EST: gi|71872083|gb|DT021138.1|DT021138
EST:     CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACG                         TTGCAATTGTATTTCAAAACCAAGC-ACCAGAGGGCAA-CA-GCCTCAGCC
genomic: CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACGgtttgtctgt ... aattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGG-CAAACAAGCCTCAGCC
EST: gi|71869160|gb|DT018215.1|DT018215
EST:     CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACG                         TTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCC
genomic: CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACGgtttgtctgt ... aattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCC-
EST: gi|110698196|gb|EE075475.1|EE075475
EST:     CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACG                         TTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
genomic: CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACGgtttgtctgt ... aattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
EST: gi|71869133|gb|DT018188.1|DT018188
EST:     CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAA-TGTTCACG                         TTGCAATTGTATTTCAAA-CCAAGCCACCAGAGGCAA-CAAGCCTCAG
genomic: CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACGgtttgtctgt ... aattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAG
EST: gi|27584644|gb|CB007339.1|CB007339
EST:     CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACG                         TTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
genomic: CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACGgtttgtctgt ... aattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
EST: gi|161712620|gb|FC061943.1|FC061943
EST:     CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACG                         TTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT
genomic: CCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACGgtttgtctgt ... aattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggattatttgtgagttttctatgacatagttccttgatgccaattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCTGCCTCTGCAGCTAATGGTACAACTGCTCCTGGTGCCCCACCAAGGCCTT
                                   ccttgat  putative branch site (score: 5)
      attatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgccaccttggtggggtttagccactgatctggttttgagaaacttttggattatttgtgagttttctatgacatagttccttgatgccaattgtacagTTGCAATTGTATTTCAAAACCAAGCCACCAGAGGCAAACAAGCCTCAGCCTGCCTCTGCAGCTAATGGTACAACTGCTCCTGGTGCCCCACCAAGGCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- -ccacctt
- - - - - ggtgggg
- - - - - - - - - - -gccactg
- - - - - - - - - - - - - - - - - - - gagaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttccttg