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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattaatattaaaaacacagtttagagctttgctgctttgcattggaaaatactggcctcatttatctgtgctgatgctcttgatcacatatcctgcagCCAATAGGAAATATTGCAGAACGGTTCCATGCTTTATGCCTGAAGGATAGCGGTGTGCTATACGAGGATCCGTATATCCAG

Basic information

species Vitis vinifera
transcript Vv06s0061g01170.t01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 19
-ttat-taatattaaaaacacagtttagagctt-tgctgctttgcattggaaaata--ctggcctcatttatctgtgctgatgctcttgatcacatatcctgcagCCAATAGGAAATATTGCAGAACGGTTCCATGCTTTATGCCTGAAGGATAGCGGTGTGCTATACGAGGATCCGTATATCCAG
   || ||| |    |      |  ||||   | | || | |||   |  ||||||   ||    ||||    | |  |  ||| | |  |  ||| |   ||||||||| ||||||||||| ||| | || |||||||| ||| |||||||||| ||||| ||||| |||||||| ||||| |||
accatgtaacaggtcactttttgactagactgtgttctccattgttctacaaaataacttgtgggcattggaatataatt-tgcacctt-ttgcatgt---gcagCCAATTGGAAATATTGCTGAAAGATTTCATGCTTTGTGCATGAAGGATAGTGGTGTTCTATATGAGGATCCTTATATTCAG

upper sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 19
ttattaatattaaaaacacagtttagagctttgctgctttgcattggaaaatactggcctc------atttatctgtgctg--atgctcttgatcacatatcc---tgcagCCAATAGGAAATATTGCAGAACGGTTCCATGCTTTATGCCTGAAGGATAGCGGTGTGCTATACGAGGATCCGTATATCCAG
          |   |  | | | | |  ||    || |   |||| |||  |  |  |  |      | || |  |   ||  ||     ||    | | | |   |||||||||| ||||||||||| ||| | || |||||||| ||| |||||||||| ||||| ||||| |||||||| ||||| |||
----------ttggactagactct-gttctccattgttcaacattagaaggttattactacaaaataacttgttggcattggaatataactggcaccttttgcatgtgcagCCAATTGGAAATATTGCTGAAAGATTTCATGCTTTGTGCGTGAAGGATAGTGGTGTTCTATATGAGGATCCTTATATTCAG
















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|34543150|gb|CF511382.1|CF511382
EST:     CAGATGCTTTGGCACTTGCACCTGTTGATGAGCAGACAAATTCCGTGCAG                         CCAATAGGAAATATTGC
genomic: CAGATGCTTTGGCACTTGCACCTGTTGATGAGCAGACAAATTCCGTGCAGgtacttcttt ... tatcctgcagCCAATAGGAAATATTGC
EST: gi|110685737|gb|EE062720.1|EE062720
EST:     CAGATGCTTTGGCACTTGCACCTGTTGATGAGCAGACAAATTCCGTGCAG                         CCAATAGGAAATATTGCAGAACGATTCCATGCTTTATGCCTGAAGGATAGC
genomic: CAGATGCTTTGGCACTTGCACCTGTTGATGAGCAGACAAATTCCGTGCAGgtacttcttt ... tatcctgcagCCAATAGGAAATATTGCAGAACGGTTCCATGCTTTATGCCTGAAGGATAGC
EST: gi|110359386|gb|EC920788.1|EC920788
EST:     CAGATGCTTTGGCACTTGCACCTGTTGATGAGCAGACAAATTCCGTGCAG                         CCAATAGGAAATATTGCAGAACGATTCCATGCTTTATGCCTGAAGGATAGC
genomic: CAGATGCTTTGGCACTTGCACCTGTTGATGAGCAGACAAATTCCGTGCAGgtacttcttt ... tatcctgcagCCAATAGGAAATATTGCAGAACGGTTCCATGCTTTATGCCTGAAGGATAGC
EST: gi|71860409|gb|DT009464.1|DT009464
EST:     CAGATGCTTTGGCACTTGCACCTGTTGATGAGCAGACAAATTCCGTGCAG                         CCAATAGGAAATATTGCAGAACGGTTCCATGCTTTATGCCTGAAGGATAGC
genomic: CAGATGCTTTGGCACTTGCACCTGTTGATGAGCAGACAAATTCCGTGCAGgtacttcttt ... tatcctgcagCCAATAGGAAATATTGCAGAACGGTTCCATGCTTTATGCCTGAAGGATAGC
EST: gi|71858407|gb|DT007462.1|DT007462
EST:     CAGATGCTTTGGCACTTGCACCTGTTGATGAGCAGACAAATTCCGTGCAG                         CCAATAGGAAATATTGCAGAACGGTTCCATGCTTTATGCCTGAAGGATAGC
genomic: CAGATGCTTTGGCACTTGCACCTGTTGATGAGCAGACAAATTCCGTGCAGgtacttcttt ... tatcctgcagCCAATAGGAAATATTGCAGAACGGTTCCATGCTTTATGCCTGAAGGATAGC
EST: gi|110379780|gb|EC944999.1|EC944999
EST:     CAGATGCTTTGGCACTTGCACCTGTTGATGAGCAGACAAATTCCGTGCAG                         CCAATAGGAAATATTGCAGAACGATTCCATGCTTTATGCCTGAAGGATAGC
genomic: CAGATGCTTTGGCACTTGCACCTGTTGATGAGCAGACAAATTCCGTGCAGgtacttcttt ... tatcctgcagCCAATAGGAAATATTGCAGAACGGTTCCATGCTTTATGCCTGAAGGATAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaaaatactggcctcatttatctgtgctgatgctcttgatcacatatcctgcagCCAATAGGAAATATTGCAGAACGGTTCCATGCTTTATGCCTGAAGGATAGCGGTGTGCTATACGAGGATCCGTATATCCAG
              tcatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattaatattaaaaacacagtttagagctttgctgctttgcattggaaaatactggcctcatttatctgtgctgatgctcttgatcacatatcctgcagCCAATAGGAAATATTGCAGAACGGTTCCATGCTTTATGCCTGAAGGATAGCGGTGTGCTATACGAGGATCCGTATATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - -aaaaaca
- - - - - - - - - - - - - - - - - tgctttg
- - - - - - - - - - - - - - - - - - - - - - -ggaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctcttg