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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAAGGATGTCCTGTAGTCTATACCTTGTATTTGAGTATATGGAGCATGATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAGgttggattcggttttttttattacctgcttttatgtgcttatttgaaaatacatataattggttgaattttgtattggttggataaacattttgaagtca...

Basic information

species Vitis vinifera
transcript Vv05s0020g01890.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA07G38140.1 (Glycine max), 5'ss of exon 2
TTCAAGGATGTCCTGTAGTCTATACCTTGTATTTGAGTATATGGAGCATGATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAGgt---tggattcg-gttttttttattacctgcttttatgtgcttatttgaaaatacatataattggttga--attttgtattggttggat--aaacattttgaagtca-------------------
|||||||||||| || ||| | |||||||| ||||| || ||||| ||||||||||||||||||||| |||||||    || |||||||||||  |||||||   |  ||       ||  ||| |      | |          || |   | |  ||| |||     |  || | || ||  | |  |   ||| | ||    | |                   
TTCAAGGATGTCATGCAGTTTGTACCTTGTCTTTGAATACATGGATCATGATTTGGCTGGACTTGCTACAAGCCCCACAATTAAGTTCACAGAGTCTCAGgtttttacatatataccttgcttagtgtaaaatctagcactagacttggttgaaatttatgattcaaaaagcatctcgtgtttctggatttggaacttcttttcttgattatagctgggtattttag

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA17G02580.1 (Glycine max), 5'ss of exon 2
TTCAAGGATGTCCTGTAGTCTATACCTTGTATTTGAGTATATGGAGCATGATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAGgt---tggat-tcggttttttttattacctgcttttatgtgcttatttgaaaatacatataatt--ggttgaattttgtattggttggat--aaacattttgaagtca-------------------
|||||||||||| || ||| | |||||||| ||||| || ||||| ||||||||||||||||||||| |||||||    || |||||||||||  |||||||   |  || |     ||  ||| |      | |          || |   | |  ||| |||       ||| || | ||  | |  |   ||| | ||    | |                   
TTCAAGGATGTCATGCAGTTTGTACCTTGTCTTTGAATACATGGATCATGATTTGGCTGGACTTGCTACAAGCCCCACAATTAAGTTCACAGAGTCTCAGgtttttacatatttacgttgcttagtgtaaaatctagcactagacttggttgaaatttatgattcaaaaaaaatcttttgtttctggatttggaacttcttttccttactatagctgggtattttag

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA15G10470.1 (Glycine max), 5'ss of exon 2
TTCAAGGATGTCCTGTAGTCTATACCTTGTATTTGAGTATATGGAGCATGATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAGgt-tggattcggttttttttattacctgcttttatgtgcttatttgaaaatacatataattggttgaattttgtattggttggataaacattttgaagtca----------------------------------
||| || ||||| || ||| |||| ||||| ||||| || |||| |||||||||||||||||||||  ||| |||||  ||||||||||||||  ||||||| | | |    |    || | | | |||| || |    || |||||||    |||| |||     |  ||| | ||  || | |   | | | || ||                                    
TTCTAGAATGTCATGCAGTTTATATCTTGTGTTTGAATACATGGTGCATGATTTGGCTGGACTTGCCACAAACCCAGCAATCAAGTTCACAGAGTCTCAGgtattggtgtattcaccttgagtgcatgctcttgt---tttgtttgaaa---tatatgattccagaatctttttctttttttggttg-cttctggaggtagtccctttttatatgctcgtatctggctattttag

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA13G28650.1 (Glycine max), 5'ss of exon 2
TTCAAGGATGTCCTGTAGTCTATACCTTGTATTTGAGTATATGGAGCATGATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAGgt-tggattcggttttttttattacctgcttttatgtgcttatttgaaaatacatataattggttgaattttgtattggttggataaacattttgaagtca----------------------------------
 || || ||||| || ||| |||| ||||| ||||| || |||| ||||||| |||||||||||||  ||| |||||  ||||||||||||||  ||||||| | | |    |    || | | | || |  | |    || |||||||   ||||| |||     |  ||| |  |  ||       | | |||| ||                                    
ATCTAGAATGTCATGCAGTTTATATCTTGTGTTTGAATACATGGTGCATGATCTGGCTGGACTTGCCACAAACCCAGCAATCAAGTTCACAGAGTCTCAGgtattggtgtattcaccttgagtgcatgttcctgt---tttgtttgaaa---catatgattcaagaatcttttttctttttttggttgcttcttgaggtggacactttttgtatgttcgtatctggatattttag

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|30126701|gb|CB912040.1|CB912040
EST:     ATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAG                         GTCAAATGTTACATGCATCAATTATTATCAGGGCTAGAACACTGTCATAAT
genomic: ATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAGgttggattcg ... gacatggcagGTCAAATGTTACATGCATCAATTATTATCAGGGCTAGAACACTGTCATAAT
EST: gi|110689805|gb|EE066351.1|EE066351
EST:     ATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAG                         GTCAAATGTTACATGCATCAATTATTATCAGGGCTAGAACACTGTCATAAT
genomic: ATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAGgttggattcg ... gacatggcagGTCAAATGTTACATGCATCAATTATTATCAGGGCTAGAACACTGTCATAAT
EST: gi|34544526|gb|CF512758.1|CF512758
EST:     ATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAG                         GTCAAATGTTACATGCATCAATTATTATCAGGGCTAGAACACTGTCATAAT
genomic: ATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAGgttggattcg ... gacatggcagGTCAAATGTTACATGCATCAATTATTATCAGGGCTAGAACACTGTCATAAT
EST: gi|71871637|gb|DT020692.1|DT020692
EST:     ATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAG                         GTCAAATGTTACATGCATCAATTATTATCAGGGCTAGAACACTGTCATAAT
genomic: ATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAGgttggattcg ... gacatggcagGTCAAATGTTACATGCATCAATTATTATCAGGGCTAGAACACTGTCATAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAAGGATGTCCTGTAGTCTATACCTTGTATTTGAGTATATGGAGCATGATTTGGCTGGACTTGCTGCAAGCCCAGGGATCAAGTTCACAGAACCTCAGgttggattcggttttttttattacctgcttttatgtgcttatttgaaaatacatataattggttgaattttgtattggttggataaacattttgaagtca

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggataaa