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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTCCCCCTCAAGTGAAGTTTCCTTTATGCACTCTTGCAGAAACCCCTAGAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAGgttaggcattgtcatttttccaagctatatatcccagtgttcttttgaactaatttctctaccatcttatttcatattttattttttag

Basic information

species Vitis vinifera
transcript Vv05s0020g02820.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g02820.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os01g16540.1 (Oryza sativa), 5'ss of exon 4
TTTTCCCCCTCAAGTGAAGTTTCCTTTATGCACTCTTGCAGAAACCCCTAGAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAGgttaggcattgtcatttttccaagctatatatcccagtgttcttttgaactaatttctctaccatcttatttcatattttattttttag
||| || || || || || ||||| ||||| || ||||| || || || |||||||| |||||||| ||||||||||| || || ||||| ||| |||||||     | |||  |  || |    || ||  | |  ||  ||  |   |      | |  ||  |     | | | |   | || |||
TTTCCCTCCCCAGGTCAAATTTCCCTTATGTACACTTGCTGAGACTCCGAGAACTGCAGCTCATTGCATTGAATATGCTCATTTGATCAAATGGAATGAGgt-----actgttctagtttctgtata-attgctctttgaactcctccccccccccccccccccccaataattaaagtcactcttgtag

upper sequence: Vv05s0020g02820.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G007915_T02 (Zea mays), 5'ss of exon 4
TTTTCCCCCTCAAGTGAAGTTTCCTTTATGCACTCTTGCAGAAACCCCTAGAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAGgttaggcattgtcatttttccaagctatatatcccagtgttcttttgaactaatttctctaccatcttatttcatattttattttttag
|||||| || || || ||||| |||||||| ||||| || || || || |||||||| ||||| || ||||| ||||| ||||| ||||| |||||||||||     ||| |   || ||   ||  ||| || |      |  | || | |   || |||| | ||    | |||||    |||||||
TTTTCCTCCACAGGTTAAGTTCCCTTTATGTACTCTCGCCGAGACACCAAGAACTGCAGCTCACTGCATTGAGTATGCTCACTTGATCAAATGGGATGAGgt-----attatt-cttctctgcgcattatttctctccagacact-gaccca---tcactactaactg---ttatattcacctttttag

upper sequence: Vv05s0020g02820.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G38770.1 (Glycine max), 5'ss of exon 4
TTTTCCCCCTCAAGTGAAGTTTCCTTTATGCACTCTTGCAGAAACCCCTAGAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAGgttaggcattgtcatttttccaagctatatatcccagtgttcttttgaactaatttctctaccatcttatttcatattttattttttag
|||||| |||||||||||||||||||| || || || || ||||||||||||||||||||||| ||||||||||| |||||||| || |||||| ||||||| |  | | ||   || |    | ||| | |   | ||| | ||       |||||      |  |||||  | |             
TTTTCCACCTCAAGTGAAGTTTCCTTTGTGTACCCTGGCTGAAACCCCTAGAACTGCTGCTCACTGTATTGAATACGCCCACTTGATTAAGTGGAATGAGgtaaatcttcgttcattctttctgttattttttataatgtccatt-------atttcaaccaaaatttattgtacag------------

upper sequence: Vv05s0020g02820.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA17G01940.2 (Glycine max), 5'ss of exon 4
TTTTCCCCCTCAAGTGAAGTTTCCTTTATGCACTCTTGCAGAAACCCCTAGAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAGgttaggcattgtcatttttccaagctatatatcccagtgttcttttgaactaatttctctaccatcttatttcatattttattttttag
|||||| |||||||| ||||||||||| || || || || |||||||||||||||||||| || |||||||||||||||||||| || |||||| ||||||| |  |   ||   || |    | ||  | |   | ||| | ||       || ||      |  ||| |  |||             
TTTTCCACCTCAAGTTAAGTTTCCTTTGTGTACCCTGGCTGAAACCCCTAGAACTGCTGCCCACTGTATTGAATATGCCCACTTGATTAAGTGGAATGAGgtaaatctccgttcattctttctgttaagt-ttgtaatgtccatt-------atatcaaccaaaatttaatgtatag------------

upper sequence: Vv05s0020g02820.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G19180.1 (Arabidopsis thaliana), 5'ss of exon 4
TTTTCCCCCTCAAGTGAAGTTTCCTTTATGCACTCTTGCAGAAACCCCTAGAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAGgttaggcattg--tcatttttccaagctatatatcccag--tgttcttttgaactaatttctctaccatcttattt----catattttattttttag-------
||| || ||||||||||||||||| || ||||||||||||||||||||||| | ||| |||||||| ||||||||||| ||  | ||  |||||||   |||  | || ||  |  ||| |  |  || | |     ||  | ||||||   | | | | |         |||||      | | |  ||| ||          
TTTCCCACCTCAAGTGAAGTTTCCGTTGTGCACTCTTGCAGAAACCCCTAGGAATGCAGCTCATTGCATTGAATATGCTCATCTTATTCAGTGGGAAACGgtatgtcaatgaattctttctgtagtctctctgaaatagactcttctttcctagtgaatacgtatttggtttattcatggtaaactcgattcttacttctgcag

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|110712941|gb|EE088425.1|EE088425
EST:     GAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAA                         GTTCATAGTGGAAAAGCATTTGATCCAG
genomic: GAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAGgttaggcatt ... tattttttagGTTCATAGTGGAAAAGCATTTGATCCAG
EST: gi|30300928|gb|CB977722.1|CB977722
EST:     GAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGANATGAG                         GTTCATAGTGGAAAAGCATTTGATCCAGATGATCCTGAACATATGGANTGA
genomic: GAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAGgttaggcatt ... tattttttagGTTCATAGTGGAAAAGCATTTGATCCAGATGATCCTGAACATATGAAATGG
EST: gi|110711880|gb|EE088865.1|EE088865
EST:     GAACTGCTGCTCATTGTATTGGATATGCCCACTTAATCAAGTGGGATGAG                         GTTCATAGTGGAAAAGCATTTGATCCAGATGATCCTGAACAT
genomic: GAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAGgttaggcatt ... tattttttagGTTCATAGTGGAAAAGCATTTGATCCAGATGATCCTGAACAT
EST: gi|110718368|gb|EE095121.1|EE095121
EST:     AACTGCTGCTCATTGTAATTGA-TAAGCCCACTTAATCAGGTGGGATGAG                         GTTCATAGTGGAAAAGCATTTGATC
genomic: AACTGCTGCTCATTGTA-TTGAATATGCCCACTTAATCAAGTGGGATGAGgttaggcatt ... tattttttagGTTCATAGTGGAAAAGCATTTGATC
EST: gi|110712191|gb|EE089528.1|EE089528
EST:     AAACTGCTGCTCATTGTATTGAATATGCCCCCTTAATCAAGTGGGAAGAA                         GTTCAAAGTGGAAAAACATTTTATCCAGATGATCCTGAACATTTGAAATGG
genomic: GAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAGgttaggcatt ... tattttttagGTTCATAGTGGAAAAGCATTTGATCCAGATGATCCTGAACATATGAAATGG
EST: gi|110711335|gb|EE087704.1|EE087704
EST:     GAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAA                         GTTCATAGTGGAAAAGCATTTGATCCAGATGATCCTGAA
genomic: GAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAGgttaggcatt ... tattttttagGTTCATAGTGGAAAAGCATTTGATCCAGATGATCCTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTCCCCCTCAAGTGAAGTTTCCTTTATGCACTCTTGCAGAAACCCCTAGAACTGCTGCTCATTGTATTGAATATGCCCACTTAATCAAGTGGGATGAGgttaggcattgtcatttttccaagctatatatcccagtgttcttttgaactaatttctctaccatcttatttcatattttattttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT