Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGTAGAATGGGCCCTTCTGATTGGAGCTAAGCCTCGAGGGCCTGGGATGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattagtatttagatttttttatcacacaagttacaaccactgtaaaaaaagaaactgctaattggtgccttcctctaaataaactgtggtttaaatattacag

Basic information

species Vitis vinifera
transcript Vv13s0019g05250.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os08g44810.1 (Oryza sativa), 5'ss of exon 5
AGATGTAGAATGGGCCCTTCTGATTGGAGCTAAGCCTCGAGGGCCTGGGATGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattagtatttagatttttttatcacacaagttaca-accactgtaaaaaaagaaactgctaattggtgccttcctctaaataaactgtggtttaaatattacag
||||| ||||||||| ||||| ||||| ||||||||  |||| ||||| ||||| ||| | | |||| ||||||| || || || || ||||||||||||||  | ||  |  || | |||  | ||  |    |  ||| |||| ||||||        |||  |        |         | | ||        |   | || | 
AGATGCAGAATGGGCTCTTCTTATTGGGGCTAAGCCCAGAGGTCCTGGAATGGAGCGATCTGCCTTACTAGATATCAACGGTCAAATCTTTGCTGAACAGgtcttcttt-tgctttgctttcctcatttcttgtggaacacaccattgtaaa--------ctgtgagcaaacctcaaaaaagggaaagacctgccaggaggcactataa

upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G129513_T01 (Zea mays), 5'ss of exon 5
AGATGTAGAATGGGCCCTTCTGATTGGAGCTAAGCCTCGAGGGCCTGGGATGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattagtatttagatttttttatcacacaagttacaaccactgtaaaaaaagaaactgctaattggtgccttcctctaaataaactgtggtttaaatattacag
||||||||| ||||||||||| ||||| |||||||| ||||| || || ||||| ||||| |   || | ||||| ||||| || || |||||||| |||||    || | |    | |  |  | ||     || ||| |   |   |||     |   |||  ||  |    |          |  ||    |||||         
AGATGTAGATTGGGCCCTTCTTATTGGCGCTAAGCCCCGAGGTCCCGGCATGGAGCGAGCTGCGCTACTGGATATCAATGGCCAAATCTTTGCTGACCAGgtttcttttgcaccctgttcctcgtttcttctcaggtaccatgccatgaaattggaagggtgccgataagcatttctgaaacttcaccctcgaatttaag--------

upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA20G33380.1 (Glycine max), 5'ss of exon 7
AGATGTAGAATGGGCCCTTCTGATTGGAGCTAAGCCTCGAGGGCCTGGGATGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattagtatttagatttttttatcacacaagttacaaccactgtaaaaaaagaaactgctaattggtgccttcctctaaataaactgtggtttaaatattacag
  ||| |||||||||  | || || || || ||||||||||| ||||| ||||||||||||||||| ||||| |||||||||||||||| ||| |  ||||||  || |  ||   ||  |||  | || ||   || |   |     ||   |||  | |  ||||       | ||| |     ||| |                 
--ATGCAGAATGGGCTTTGCTAATAGGTGC-AAGCCTCGAGGACCTGGAATGGAACGAGCAGACTTGTTAGACATAAATGGGCAGATTTATGCAGCGCAGgtaaaatgataat---gaaatttaaaccatacttattgctttctgctaaagtgaagttaattataatgacattataccttttgtacaacag-----------------

upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G34150.3 (Glycine max), 5'ss of exon 5
AGATGTAGAATGGGCCCTTCTGATTGGAGCTAAGCCTCGAGGGCCTGGGATGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattagtatttagatttttttatcacacaagttacaa-ccactgtaaaaaaagaaactgctaattggtgccttcctctaaata-aactgtggtttaaatattacag
||||| |||||||||  | || || || || || |||||||| ||||| ||||||||||||||||| ||||| |||||||||||||||| ||| |  ||||||  |  | || | ||||||    |||| |    || |   || ||  |    |   || |    | ||      | |  |   || ||| |                 
AGATGCAGAATGGGCTTTGCTAATAGGTGCAAAACCTCGAGGACCTGGAATGGAACGAGCAGACTTGTTAGACATAAATGGGCAGATTTATGCAGCGCAGgtaaaacga-taatcagatttaa--atcatatttattgctttccgctaaagtgtagttaattat--actgacattataccttttgtacaacag-----------------

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|110728729|gb|EE104550.1|EE104550
EST:     TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAG                         GGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
genomic: TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattag ... aatattacagGGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
EST: gi|34550427|gb|CF518645.1|CF518645
EST:     TTTTGCTGAACAG                         GGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
genomic: TTTTGCTGAACAGgtactattag ... aatattacagGGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
EST: gi|351028003|gb|FQ425904.1|FQ425904
EST:     TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAG                         GGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
genomic: TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattag ... aatattacagGGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
EST: gi|32249928|gb|CD715747.1|CD715747
EST:     TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAG                         GGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
genomic: TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattag ... aatattacagGGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
EST: gi|30137894|gb|CB923232.1|CB923232
EST:     TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAG                         GGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
genomic: TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattag ... aatattacagGGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
EST: gi|27578522|gb|CB001217.1|CB001217
EST:     TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAG                         GGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
genomic: TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattag ... aatattacagGGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
EST: gi|37190333|gb|CF609682.1|CF609682
EST:     TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAG                         GGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
genomic: TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattag ... aatattacagGGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
EST: gi|110392317|gb|EC957652.1|EC957652
EST:     TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAG                         GGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
genomic: TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattag ... aatattacagGGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
EST: gi|18458011|gb|BM436289.1|BM436289
EST:     TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAG                         GGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
genomic: TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattag ... aatattacagGGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
EST: gi|29785366|gb|CB342287.2|CB342287
EST:     TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAG                         GGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG
genomic: TGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattag ... aatattacagGGAAAAGCTCTCAATGCTGTGGCATCCCGTAATGTCAAAGTGATGGTAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGTAGAATGGGCCCTTCTGATTGGAGCTAAGCCTCGAGGGCCTGGGATGGAACGAGCAGACTTATTAGATATAAATGGGCAGATTTTTGCTGAACAGgtactattagtatttagatttttttatcacacaagttacaaccactgtaaaaaaagaaactgctaattggtgccttcctctaaataaactgtggtttaaatattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT