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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTTTACACAATTACGCTTCACATATGAACAAGAGAGCCATCCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTGgtactgttcctgaatctttccccctctttttggaggaattaaactaggaaaaaataaaataaataaataaataaataaaaaataaaaaaagtaatagagc...

Basic information

species Vitis vinifera
transcript Vv05s0020g04100.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04100.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G079389_T01 (Zea mays), 5'ss of exon 16
ATGTTTACACAATTACGCTTCACATATGAACAAGAGAGCCATCCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTGgta-----ctgttcctgaatctttccccctctttttggaggaattaaactaggaaaaaataaaataaataaataaataaataaaaaataaaaaaagtaatagagc
|||||||| || ||||| || |||||||| ||||| ||||| || ||||||||||| ||||| ||||  ||||  || || ||||| ||  ||||      || |  |  ||   |    | |  |||             |    ||| || | |    | | |   |   |||||| |   |  | |  |     
ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAGTTCTTCATCCCATATGCATGGCGCCTTGTCCTATCACGGGGgtaatcatttgctgttatatagatgattcacagttttttactccctccgtttataaatatgacactgttgacttttt---taaaaactttgatcattcgtctt--

upper sequence: Vv05s0020g04100.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA20G28880.1 (Glycine max), 5'ss of exon 15
ATGTTTACACAATTACGCTTCACATATGAACAAGAGAGCCATCCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTGgtactgttcctgaatctttccccctctttttggaggaattaaactaggaaaaaataaaataaataaataaataaataaaaaataaaaaaagtaatagagc----
|||||||| ||| | ||||||||||||||||||||||| |||||||||||||| |||||||| ||||| |||||||||||||||||||  |||||   |||||| | |||| |   ||   |||    ||     |||   | || ||   ||     | |  |  |       |       ||  ||   |    
ATGTTTACTCAACTGCGCTTCACATATGAACAAGAGAGTCATCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTTCTATCCCATTGgtatgattcctggagcttttctattcacattgtctcaa---ggctacatataattattttactcttacattttga-gttgtgttggtcttgttttatttcattc

upper sequence: Vv05s0020g04100.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA10G38920.2 (Glycine max), 5'ss of exon 16
ATGTTTACACAATTACGCTTCACATATGAACAAGAGAGCCATCCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTGgtactgttcctgaatctttccccctctttttggaggaattaaactaggaaaaaataaaataaataaataaataaataaaaaataaaaaaagtaatagagc---------
|||||||| ||| | ||||||||||||||||||||||| |||||||||||||| |||||||| ||||| ||||||||||| |||||||| |||||   |||||| | |||| |   ||           |||    || |   | ||| ||| | |  |    || ||    |||       |   ||   |         
ATGTTTACTCAACTGCGCTTCACATATGAACAAGAGAGTCATCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTGCTATCCCGTTGgtatgattcctggagcttttctattcac---------attgtcttaaggctacatataattattttactcttacattttgaattgtgttggccttatttcatttcatta

upper sequence: Vv05s0020g04100.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA15G24080.1 (Glycine max), 5'ss of exon 18
ATGTTTACACAATTACGCTTCACATATGAACAAGAGAGCCATCCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTGgtactgttcctgaa--tctttccccctctttttggaggaattaaactaggaaaaaataaaataaataaataaataaataaaaaataaaaaaagtaatagagc
|||||||| ||| | | ||||||||||||||||||||| || | |||||||||||||||||| ||||| ||||||||||| |||||| |  ||||  ||||  ||   ||||   | ||    |||  |  |||       |      |   |||  |  |  | |   |      |||   | ||  |     
ATGTTTACTCAACTTCACTTCACATATGAACAAGAGAGTCACCAAGAGGAGTTCTTTATCCCATATGTCTGGCAGCTAGTACTATCCAGACGgtatggttctagagattcttattcacttacattgtggctatttgtaactgttttgctcttatagtttga--actttgttgttcttaatgcatgtggtttcca

upper sequence: Vv05s0020g04100.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA10G00550.1 (Glycine max), 5'ss of exon 16
ATGTTTACACAATTACGCTTCACATATGAACAAGAGAGCCATCCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTGgtactgttcctgaatctttccccctctttttggaggaattaaactaggaaaaaataaaataaataaataaataaataaaaaataaaaaaagtaatagagc
|||||||| ||| | |  |||||||||||||||||||| || ||||||||||| |||||||| ||||| ||||||||||| |||||| | |||||  ||||  ||   | |       |   |       |     |  | ||   |     |  |  |  |  || |      |    || | |   |   
ATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTACTATCCAGATGgtatggttctagagattcttatttattcacttacttcgtggctatttgtaactgtttttcacttgtagtatgaactttgttgttcttaatgcatgtggtt

upper sequence: Vv05s0020g04100.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: AT1G04200.1 (Arabidopsis thaliana), 5'ss of exon 16
ATGTTTACACAATTACGCTTCACATATGAACAAGAGAGCCATCCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTGgtactgttcctga--------atctttccccctctttttggaggaattaa-actaggaaaaaataaaataaataaataaataaataaaaaa-taaaaaaagtaatagagc----
|||||||| ||  | | |||| ||||||||||||||||||| || || ||||| ||||| || ||||| ||||| |||| | | ||||| |||||     ||| |        | |||  | | |  || |  |  | ||   |  | ||     ||| | | |  |      | ||       | |      |  | |  |    
ATGTTTACTCAGCTTCACTTCTCATATGAACAAGAGAGCCACCCGGAAGAGTTTTTTATTCCATATGTTTGGCAACTAGCTTTTTCCCGATGgtaaccaacctaatataaacaaacttatctctttcttctatactacttgtcatcacgatgttgtaacaaagaacaccgctcacattcctctctcacgtttctttttgttcgcag

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|352769602|gb|FQ468530.1|FQ468530
EST:     CCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTG                         TGGATTCAGCTTTAATGCCAGTACCATAAACTTGTTCCCAGTTGATCAGCC
genomic: CCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTGgtactgttcc ... tttttttcagTGGATTCAGCTTTAATGCCAGTACCATAAACTTGTTCCCAGTTGATCAGCC
EST: gi|351024882|gb|FQ433299.1|FQ433299
EST:     CCAGAGGGGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTG                         TGGATTCAGCTTTAATGCCAGTACCATAAACTTGTTCCCAGTTGATCAGCC
genomic: CCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTGgtactgttcc ... tttttttcagTGGATTCAGCTTTAATGCCAGTACCATAAACTTGTTCCCAGTTGATCAGCC
EST: gi|352780976|gb|FQ466289.1|FQ466289
EST:     CCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTG                         TGGATTCAGCTTTAATGCCAGTACCATAAACTTGTTCCCAGTTGATCAGCC
genomic: CCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTGgtactgttcc ... tttttttcagTGGATTCAGCTTTAATGCCAGTACCATAAACTTGTTCCCAGTTGATCAGCC
EST: gi|110362374|gb|EC925903.1|EC925903
EST:     CCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTG                         TGGATTCAGCTTTAATGCCAGTACCATAAACTTGTTCCCAGTTGATCAGCC
genomic: CCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTGgtactgttcc ... tttttttcagTGGATTCAGCTTTAATGCCAGTACCATAAACTTGTTCCCAGTTGATCAGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTTTACACAATTACGCTTCACATATGAACAAGAGAGCCATCCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTGgtactgttcctgaatctttccccctctttttggaggaattaaactaggaaaaaataaaataaataaataaataaataaaaaataaaaaaagtaatagagc

- - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa