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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaatgtctgaagatggctgattcttcacattgtactttggtttaactttttttgaggccacgatttagatgcttcctcataaatttcattttctgaagGTCCTCTATGCATTATTCAACCTCTGCAAGATAAATAAGAGGAGGCAAGAACAAGCAGCTGAAAATGGAATCATTCCACACTTGATGCATTTTATAATGT

Basic information

species Vitis vinifera
transcript Vv01s0011g02270.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 21
------ttaaatgtctgaagatggctgattcttcacattgtactttggtttaactttttttgaggccacgatttagatgcttcctcataaatttcattttctgaagGTCCTCTATGCATTATTCAACCTCTGCAAGATAAATAAGAGGAGGCAAGAACAAGCAGCTGAAAATGGAATCATTCCACACTTGATGCATTTTATAATGT
        |||||||  ||||  | ||  | |||| | | |    | | |   |    |||     |||  | ||      ||     || |||    |  |  |||||||| ||||  | ||||| || |||||||| ||||| || || || |||||||||||||||||||| ||||| || ||||| ||| ||||| | ||||
ttagggacaaatgtc--aagacagttggctattcagaatttgaaataggtctgcacgatttctcagcacattataa----ctctatgcaattttttgctgttttagGTCCTCAATGCTCTGTTCAATCTTTGCAAGATCAATAAAAGAAGACAGGAACAAGCAGCTGAAAATGGGATCATCCCTCACTTAATGAATTTTGTCATGT

upper sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA11G10810.1 (Glycine max), 3'ss of exon 23
-----ttaaatgtctgaagatggctgattcttcacattgtactttggtttaactttttttgaggccacgatttagatgcttcctcataaatttcattttctgaagGTCCTCTATGCATTATTCAACCTCTGCAAGATAAATAAGAGGAGGCAAGAACAAGCAGCTGAAAATGGAATCATTCCACACTTGATGCATTTTATAATGT
      ||| |||||| |  |   |  || | |    | |   ||| ||   |    ||  |  ||  | || ||     || || |||||||||||||||  ||||| |  | ||| |||||||  | |||||||||||||||||||| |||||||||||||||||||||||||||||||| || |||||||  || || |  |
tttgtgtaattgtctgtaatt--tttgttgtcctttctttgtcttgcttcgtcagccttctaaacctggcttgag---tctcatcttaaatttcattttctatagGTCTTGAACGCACTATTCAATTTATGCAAGATAAATAAGAGGAGACAAGAACAAGCAGCTGAAAATGGAATCATTCCCCATTTGATGCTATTCATCACAT

upper sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA12G03090.1 (Glycine max), 3'ss of exon 23
ttaaatgtctgaagatggctgattcttcacattgtactttggtttaactttttttgaggccacgatttagatg--cttcctcataaatttcattttctgaagGTCCTCTATGCATTATTCAACCTCTGCAAGATAAATAAGAGGAGGCAAGAACAAGCAGCTGAAAATGGAATCATTCCACACTTGATGCATTTTATAATGT
 ||| | |||| |  |   |  || | |    | |   ||| ||   |    ||  |  ||  | ||| | ||  | || || |  |||||  |||||  ||||| |  | ||| |||||||  | |||||||||||||||||||| |||||||||||||||||||||||||||||||| || |||||||| || || |  |
gtaattatctgtaatt--tttgttgtcctttctttgtcttgcttcgtcagccttctaaaccgggctttggttgagcctcatctttcatttctctttctatagGTCTTGAACGCACTATTCAATTTATGCAAGATAAATAAGAGGAGACAAGAACAAGCAGCTGAAAATGGAATCATTCCCCATTTGATGCAATTCATCACAT

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|110378264|gb|EC943387.1|EC943387
EST:     CAAACCTTGAACTCAAAGAAGGGCCTCTTGTATTTCAAATACATTATGAG                         GTCCTCTATGCATTATTCAACCTCTGCAAGATAAATAAGAGGAGGCAAGAA
genomic: CAAACCTTGAACTCAAAGAAGGGCCTCTTGTATTTCAAATACATTATGAGgtaaactttc ... ttttctgaagGTCCTCTATGCATTATTCAACCTCTGCAAGATAAATAAGAGGAGGCAAGAA
EST: gi|110385202|gb|EC949705.1|EC949705
EST:     CAAACCTTGAACTCAAAGAAGGGCCTCTTGTATTTCAAATACATTATGAG                         GTCCTCTATGCATTATTCAACCTCTGCAAGATAAATAAGAGGAGGCAAGAA
genomic: CAAACCTTGAACTCAAAGAAGGGCCTCTTGTATTTCAAATACATTATGAGgtaaactttc ... ttttctgaagGTCCTCTATGCATTATTCAACCTCTGCAAGATAAATAAGAGGAGGCAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactttttttgaggccacgatttagatgcttcctcataaatttcattttctgaagGTCCTCTATGCATTATTCAACCTCTGCAAGATAAATAAGAGGAGGCAAGAACAAGCAGCTGAAAATGGAATCATTCCACACTTGATGCATTTTATAATGT
 gtttaac  putative branch site (score: 3)
                                        tttcattttct  putative PPT
                                 tcataaatttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaatgtctgaagatggctgattcttcacattgtactttggtttaactttttttgaggccacgatttagatgcttcctcataaatttcattttctgaagGTCCTCTATGCATTATTCAACCTCTGCAAGATAAATAAGAGGAGGCAAGAACAAGCAGCTGAAAATGGAATCATTCCACACTTGATGCATTTTATAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - -tgtctga
- - - - - - - -tggctga
- - - - - - - - - - - - cttcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gaggcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcctc