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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatttttgcacccattgttggttgttctaatatgttagagattatttgttgtgaattgtcttgccaccttgccttacatgcttctttaatgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTACTCCTTGAATATGTTCAAAGATTTTGTTCCTATGTGTGTTTTTTCTGAGA

Basic information

species Vitis vinifera
transcript Vv18s0001g13370.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g13370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g43450.1 (Oryza sativa), 3'ss of exon 1
agaatttttgcacccattgttggttgttctaatatgttagagattatttgttgtga--attgtcttgccaccttgccttacatgcttctttaatgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTACTCCTTGAATATGTTCAAAGATTTTGTTCCTATGTGTGTTTTTTCTGAGA
     ||   |   |  |||| ||| |  | |    ||     ||  |||| |||   || ||     ||       | ||||| | || |    || ||||||||  ||||| ||| ||   |||    ||   ||||  ||||| ||||||||||||||||||| ||| |||||||| || ||||||||||| |||||| 
-attgttccccgttctatgttagtt-tcatcactcatttctttttgcttgtggtgcctatagttacatcattcattataacatggtgctattggcatggcagTTCAAGATGGAGATGGCTCAAACTAACACTGGCAATACACCAAAGAGTTACTCCTTGAATATGTCCAAGGATTTTGTACCAATGTGTGTTTTCTCTGAGT

upper sequence: Vv18s0001g13370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g56550.3 (Oryza sativa), 3'ss of exon 1
agaatttttgcacccattgttggttgttctaat-atgttagagattatttg-ttgtgaattgtcttgccacct-tgccttacatgcttctttaatgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTACTCCTTGAATATGTTCAAAGATTTTGTTCCTATGTGTGTTTTTTCTGAGA
    ||| || |  | |   |  | ||   |||    |||  | || | |  ||||  |    |      ||| |  |||| ||| |  |      ||| |||||||  ||||| ||| ||   || ||   |   ||||  ||||| |||||||||||||| |||||||| |||||||| || |||||||| ||||||||  
---ttttctgtattcttgtataatagtagaaattgacttacggcttctatacttgtacacacacccagtgcctgtttcttatatgttgttagtgaaataacagTTCAAGATGGAGATGGCTCAAACAGGCAATGGCAATACACCAAAGAGTTACTCCTTGAACATGTTCAAGGATTTTGTGCCAATGTGTGTCTTTTCTGAAT

upper sequence: Vv18s0001g13370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G060284_T02 (Zea mays), 3'ss of exon 1
agaatttttgcacccattgttggttgttctaatatgttagagattatttgttgtgaattgtcttgccaccttgc---cttacatgcttctttaatgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTACTCCTTGAATATGTTCAAAGATTTTGTTCCTATGTGTGTTTTTTCTGAGA
   ||  | | |  | ||| |  |  | ||  |   |    | || |||  |||  || || ||| |||||  |   |||||||  | || |    ||  |||||||  |||||| || ||   |||    |    ||||  || || || ||||| |||||||||||||||||||| ||||||||||||||||| || ||  
--cataatcgaattccttggtattaatgctgctcactatctgtttgtttcatgtatat-gttttggcacctaccattcttacatcatgctattgcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTACTCTTTGAATATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAAT

upper sequence: Vv18s0001g13370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G049091_T01 (Zea mays), 3'ss of exon 1
agaatttttgcacccattgttggttgttcta-atatgttagagattatttgttgtgaattgtcttgccaccttgccttacatgcttctttaatgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTACTCCTTGAATATGTTCAAAGATTTTGTTCCTATGTGTGTTTTTTCTGAGA
 ||    |||       || |  |  || |   | ||||  | ||   |  |      || |  ||||       ||||||   | || | |  |   |||||||  |||||  || |    |||    ||   ||||  || || || ||||| |||||||||||||||||||| || |||||||||||||| || ||  
-gatccgttggtgttgatgcttctcattatgtgtttgttttatatatatcatctctgcttttggtgcctgtcattcttacaccatgctattacaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTACTCTTTGAATATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAAT

upper sequence: Vv18s0001g13370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G03030.1 (Glycine max), 3'ss of exon 1
-----agaatttttgcacccattgttggttgttctaatatgttagagattatttgttgtgaattgtcttgccaccttgccttacatgcttctttaatgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTACTCCTTGAATATGTTCAAAGATTTTGTTCCTATGTGTGTTTTTTCTGAGA
     |||||| |  ||       |  ||  |||| || |  ||    ||  ||||  |||  |         | |||  ||| |    |   |||| ||  ||||| |||||||| ||| ||||| | |  |||   ||||||||||||| ||| || ||||||||||| ||||| ||||||||||||||||| || || ||||
cttctagaattgtcacagtatagatatgtgcttctgat-taatatttgttgcttgtattgatgtaagagagt-cattgatttataa---ttcataattatgtcagTTTACAATGGAGATGGCTGGCTCCGAAGCTGTGAATATGCCAAAAACTTATTCATTGAATATGTTTAAAGACTTTGTTCCTATGTGTGTCTTCTCCGAGA

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|110712491|gb|EE090172.1|EE090172
EST:     TCGTCCTCTCCCTCGATCCTCTCCGCTCCGAAGATCCCTCTGCGCTGGAG                         TTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTAC
genomic: TCGTCCTCTCCCTCGATCCTCTCCGCTCCGAAGATCCCTCTGCGCTGGAGgtacctttcc ... atgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTAC
EST: gi|33410257|gb|CF215884.1|CF215884
EST:     TCGTCCTCTCCCTCGATCCTCTCCGCTCCGAAGATCCCTCTGCGCTGGAG                         TTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTAC
genomic: TCGTCCTCTCCCTCGATCCTCTCCGCTCCGAAGATCCCTCTGCGCTGGAGgtacctttcc ... atgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTAC
EST: gi|71876173|gb|DT025228.1|DT025228
EST:     TCGTCCTCTCCCTCGATCCTCTCCGCTCCGAAGATCCCTCTGCGCTGGAG                         TTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTAC
genomic: TCGTCCTCTCCCTCGATCCTCTCCGCTCCGAAGATCCCTCTGCGCTGGAGgtacctttcc ... atgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTAC
EST: gi|110713762|gb|EE089967.1|EE089967
EST:     TCGTCCTCTCCCTCGATCCTCTCCGCTCCGAAGATCCCTCTGCGCTGGAG                         TTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTAC
genomic: TCGTCCTCTCCCTCGATCCTCTCCGCTCCGAAGATCCCTCTGCGCTGGAGgtacctttcc ... atgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTAC
EST: gi|110702596|gb|EE081122.1|EE081122
EST:     CTGCGCTGGAG                         TTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTAC
genomic: CTGCGCTGGAGgtacctttcc ... atgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgttgtgaattgtcttgccaccttgccttacatgcttctttaatgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTACTCCTTGAATATGTTCAAAGATTTTGTTCCTATGTGTGTTTTTTCTGAGA
                                         tttaatgata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatttttgcacccattgttggttgttctaatatgttagagattatttgttgtgaattgtcttgccaccttgccttacatgcttctttaatgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTACTCCTTGAATATGTTCAAAGATTTTGTTCCTATGTGTGTTTTTTCTGAGA

- - - - -gcaccca
- - - - - - - - - - tggttgt
- - - - - - - - - - - - - - - - - - - - - - - - tgttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgct