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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTTGCTCAGATGGAAAAGAGGGTGGTTATGGCAGAAACAATGTTAGAAGCTACCTTGCAATACCAATCTGGGCAAGTTAAAGCACAGCCTTCTCCCCGgtatgttgtcaactttgccgataaagatttcttcctctgtgcagtttcatctttgttattgactagatgaatctatcactgtgttcaatatctgttgtga...

Basic information

species Vitis vinifera
transcript Vv13s0067g03420.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g03420.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G094951_T01 (Zea mays), 5'ss of exon 16
CTCTTGCTCAGATGGAAAAGAGGGTGGTTATGGCAGAAACAATGTTAGAAGCTACCTTGCAATACCAATCTGGGCAAGTTAAAGCACAGCCTTCTCCCCGgtatgttgtcaactttgccgataaagatttcttcctctgtgcagtttcatctttg---ttattgactagatgaatctatcactgtgttcaatat-ctgttgtga------
         | ||||| ||  | |  || |||||||||||||||||||| |||||  |||| ||||||||| | ||    ||||||| | |  ||  ||  | |       |  |      ||   ||| |||  | || |  |    |   ||     ||   |  ||     |||| ||      ||| | | || |||  |      
---------AAATGGAGAACCGAGCTGTAATGGCAGAAACAATGTTAGAGGCTACACTGCAGTACCAATCTAGCCAGCAGAAAGCACTGTCCCCTTGCCCTTCTCCAAGgtatctcaatcttatctatt-cttagtgtgagatggacaactcttaaaactagcaataaggcagttctaacataccagtcatttttctattgctaacttct

upper sequence: Vv13s0067g03420.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA20G38810.1 (Glycine max), 5'ss of exon 16
CTCTTGCTCAGATGGAAAAGAGGGTGGTTATGGCAGAAACAATGTTAGAAGCTACCTTGCAATACCAATCTGGGCAAGTTAAAGCACAGCCTTCTCCCCGgtatgttgtcaactttgccgataaagatttcttcctctgtgcagtttcatctttgttattgactagatgaatctatcactgtgttcaatatctgttgtga
| |||||| | ||||| |||||||  |||||||||||| | ||| | || ||||| ||||| ||||||||||| ||||||||||  |  |  ||||| |||||| |       ||||     ||| ||  ||                                                                    
CACTTGCTGAAATGGAGAAGAGGGCAGTTATGGCAGAATCTATGCTGGAGGCTACATTGCAGTACCAATCTGGCCAAGTTAAAGTGCTACAATCTCCACGgtatataagt--ttttg-----aaatatccctgtag----------------------------------------------------------------

upper sequence: Vv13s0067g03420.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: AT2G39280.1 (Arabidopsis thaliana), 5'ss of exon 16
CTCTTGCTCAGATGGAAAAGAGGGTGGTTATGGCAGAAACAATGTTAGAAGCTACCTTGCAATACCAATCTGGGCAAGTTAAAGCACAGCCTTCTCCCCGgtatgttgtcaactttgccgataaagatttcttcctctgtgcagtttcatctttgttattgactagatgaatctatcactgtgtt-caatatctgttgtga
|||| ||  |||||||  ||||||  |||||||||||  | ||||| || || || ||||| || |||||||| |||||||||||||| ||||| || |||| ||||      || ||  |||   | |        |||  |     |  |||   ||||  |  || ||   | || | | || |   | || ||  | 
CTCTCGCGGAGATGGAGGAGAGGGCAGTTATGGCAGAGTCCATGTTGGAGGCGACTTTGCAGTATCAATCTGGCCAAGTTAAAGCACAACCTTCACCACGgtctgtttct---ttggcatatatcaagtgaacttggtgtagaaaactagattttccattgggtgcattaagtcaccattatttttctgaaacttttcag-

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|30136499|gb|CB921837.1|CB921837
EST:     GCTACCTTGCAATACCAATCTGGGCAAGTTAAAGCACAGCCTTCTCCCCG                         ATCACATCAAGATTCCTCTTCAGCACGAAGCAATCAAGAAACACCACAAGA
genomic: GCTACCTTGCAATACCAATCTGGGCAAGTTAAAGCACAGCCTTCTCCCCGgtatgttgtc ... ttgattgtagATCACATCAAGATTCCTCTTCAGCACGAAGCAATCAAGAAACACCACAAGA
EST: gi|30135773|gb|CB921111.1|CB921111
EST:     GCTACCTTGCAATACCAATCTGGGCAAGTTAAAGCACAGCCTTCTCCCCG                         ATCACATCAAGATTCCTCTTCAGCACGAAGCAATCAAGAAACACCACAAGA
genomic: GCTACCTTGCAATACCAATCTGGGCAAGTTAAAGCACAGCCTTCTCCCCGgtatgttgtc ... ttgattgtagATCACATCAAGATTCCTCTTCAGCACGAAGCAATCAAGAAACACCACAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTTGCTCAGATGGAAAAGAGGGTGGTTATGGCAGAAACAATGTTAGAAGCTACCTTGCAATACCAATCTGGGCAAGTTAAAGCACAGCCTTCTCCCCGgtatgttgtcaactttgccgataaagatttcttcctctgtgcagtttcatctttgttattgactagatgaatctatcactgtgttcaatatctgttgtga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gataaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcctc