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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTAAAGCAGATCAATAACTGGTTCATCAACCAAAGGAAACGGAATTGGCACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaatgctgtgttgcatttctggaatctgctttccttgagagccttttgccaactttaatttggaaaag

Basic information

species Vitis vinifera
transcript Vv11s0118g00800.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0118g00800.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA09G12820.1 (Glycine max), 5'ss of exon 5
----TTTAAAGCAGATCAATAACTGGTTCATCAACCAAAGGAAACGGAATTGGCACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaatgctgtgttgcatttctggaatctgctttccttgagagcc----ttttgccaactttaatttggaaaag--------------------
     ||||||||||| |||||||||||||| || ||||| ||| |||||||||| |  |||||||| ||||||   |  |  || | ||| || ||||||| || |   || |    |  |  |||| |||| |     ||    |||| |     |  |   |  || || |    |||                     
TGCAATTAAAGCAGATAAATAACTGGTTCATAAATCAAAGAAAAAGGAATTGGCATACTAATCCTTCGTCTTCTAGTGGCTCCAAAAGCAAACGCAAGAGgtgggttt-ctagtttcttagtatatttttgga-ttaaagttagaagagatcaaaggtacttttactttcaaatcaataaaaattttcttctcattttatgt

upper sequence: Vv11s0118g00800.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA15G24350.1 (Glycine max), 5'ss of exon 7
----TTTAAAGCAGATCAATAACTGGTTCATCAACCAAAGGAAACGGAATTGGCACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaatgctgtgttgcatttctggaatctgcttt-ccttgagagccttttgccaactttaatttggaaaag---------------------
     ||||||||||| |||||||||||||| || ||||| ||| |||||||||| |  ||||| || ||||||   |  |  || | ||| || ||||||| || |  |   | |||| |   ||| ||   |  | |       | |   | ||    |  |||| || ||  | |                      
TGCAATTAAAGCAGATAAATAACTGGTTCATAAATCAAAGAAAAAGGAATTGGCATACTAATCCGTCGTCTTCTAGTGGCTCCAAAAGCAAACGCAAGAGgtgggtttctagtttctgtttataattacttttacttccaaagtaataatttctttccttctccttttatgtgttagaacatattcttgcattggaatat

upper sequence: Vv11s0118g00800.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA17G11330.1 (Glycine max), 5'ss of exon 5
-TTTAAAGCAGATCAATAACTGGTTCATCAACCAAAGGAAACGGAATTGGCAC---AGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaatgctgtgttgcatttc-tggaatctgctttccttgag----agccttttgccaactttaatttggaaaag-----------------
  ||||||||||| ||||| |||||||| || ||||||||| |||| |||||    |  || || ||||| |||      |  || | |||||| |||||||||| | |||    ||   ||            || |  | |  ||| |    |   |||  | |||  |  |   ||                     
AATTAAAGCAGATAAATAATTGGTTCATAAATCAAAGGAAAAGGAACTGGCATACAAATAACCCCTCATCCTCTAGCAACTCCAAAAGCAAGCGCAAGAGgtaggttaattgtcacttctttcttccaaacaatatatattattattgtggcttaatgtttgacaaaccatcctcaagatgcattttatggcttaattaa

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|110357959|gb|EC921831.1|EC921831
EST:     ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCG-AA-A-G-AG                         AAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
genomic: ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaat ... tttggaaaagAAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
EST: gi|351026924|gb|FQ436577.1|FQ436577
EST:     ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAG--A-                         A-GTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
genomic: ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaat ... tttggaaaagAAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
EST: gi|110403174|gb|EC964453.1|EC964453
EST:     ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCG--A-A---AG                         -AGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
genomic: ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaat ... tttggaaaagAAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
EST: gi|351033382|gb|FQ446614.1|FQ446614
EST:     ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCG-AA-A-G-AG                         AAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
genomic: ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaat ... tttggaaaagAAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
EST: gi|349832281|gb|FQ420842.1|FQ420842
EST:     ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCG-AA-A-G-AG                         AAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
genomic: ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaat ... tttggaaaagAAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
EST: gi|349823669|gb|FQ415079.1|FQ415079
EST:     ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCG-AA-A-G-AG                         AAGTAATACAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
genomic: ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaat ... tttggaaaagAAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
EST: gi|110358258|gb|EC922342.1|EC922342
EST:     ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCG-AA-A-G-AG                         AAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
genomic: ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaat ... tttggaaaagAAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
EST: gi|351012554|gb|FQ430118.1|FQ430118
EST:     ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCG-AA-A-G-AG                         AAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
genomic: ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaat ... tttggaaaagAAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
EST: gi|351023592|gb|FQ432975.1|FQ432975
EST:     ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCG-AA-A-G-AG                         AAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
genomic: ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaat ... tttggaaaagAAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
EST: gi|351056126|gb|FQ453588.1|FQ453588
EST:     ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAG--A-                         A-GTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
genomic: ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaat ... tttggaaaagAAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
EST: gi|349830594|gb|FQ416892.1|FQ416892
EST:     ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCG-AA-A-G-AG                         AAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT
genomic: ACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaat ... tttggaaaagAAGTAATGCAGGTGAAATCAACAATGATCACTTTTTGTAAATGGACAAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTAAAGCAGATCAATAACTGGTTCATCAACCAAAGGAAACGGAATTGGCACAGCAATCCTTCATCTTCTGCAGTTTTGAAGACCAAGCGAAAGAGGTAGgctgattaatgctgtgttgcatttctggaatctgctttccttgagagccttttgccaactttaatttggaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG