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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggatctctctctcttttcttttccttctatttctccgatgattgtgttttgggttatttgattaaaaggatgaaatcttttccttctatttctc...

Basic information

species Vitis vinifera
transcript Vv13s0019g03600.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os05g38820.5 (Oryza sativa), 5'ss of exon 1
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggatctctctctcttttcttttccttctatttctccgatgattgtgttttgggttattt-gattaaaaggatgaaatcttttccttctatttctc------------------------------------------------------
|||||||||||||  | ||||| || || |||||||||||||| || ||||| || || || |||||||||||||||||||||   ||||||||||||||||  |  | || | |||    | |     ||| |  |   |       | || | ||  || ||| || |     | |   | ||  |  ||  | || ||                                                      
TCATGAAGAAGGCCATCCCGGCCAACGGGAAGATCGCCAAGGACGCCAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACCAGCGAgtgagtcg-tcgccctcgtcctcccccctcttgtgctctgct--ctgctctgctctgtcttcttttgagttttgagctttgagctcgttgtttgacttgtcgttggcggcgatgagatgtgactgggtttttgttgtggtggggcaacattacag

upper sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os01g61810.3 (Oryza sativa), 5'ss of exon 2
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacg-cggatctctctctcttttcttttccttctatttctccgatgattgtgttttgggttatttgattaaaaggatgaaatcttttccttctatttctc------------------------
|||||||||||||  | ||||| || || |||||||||||||| || ||||| ||  | || ||||||||||| |||||||||   ||| ||||||||||||  | | |  |   |||  |    |  |||| |  |  |  |    |   | ||||| | |  ||| || |  |  |||  |   ||   | | |   |                         
TCATGAAGAAGGCCGTCCCGGCGAACGGCAAGATCGCCAAGGACGCCAAGGAGACCCTGCAGGAGTGCGTCTCGGAGTTCATCTCCTTCGTCACCAGCGAgtgagtctgcgcgggctcggtaccgtgatcctgccctccccac----accttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacag

upper sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggatctctctctcttttcttttccttctatttctcc----gatgattgtgttttgggttatttgattaaaa--ggatgaaatcttttccttctatttctc------------------------------
|||||||||||||  | |||||||| || |||||||||||||| || ||||| || || || |||||||||||||||||||||   |||||||| |||||||| | |  ||     |   |  || || ||| |  ||  |     |   |||  |  | | |||    | || |    || ||   | || |  |    | ||                                
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcag

upper sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G064426_T02 (Zea mays), 5'ss of exon 2
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgta-----------cgcggat--ctctctctcttttcttttccttctatttctccgat----gattgtgttttgggttatttgattaaaaggatgaaatcttttccttctatttctc-------------------------------
|||||||||||||  | |||||||| || |||||||||||||| || ||||| || || || ||||||||||| |||||||||   |||||||| ||||||||           ||||| |  ||||  ||||| | ||| | |   || |     ||      | | |||| |          || |    | |     ||||   |  | || ||                               
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCGGAGTTCATCTCCTTCATCACTAGCGAgtaagtccctcggccgcggctgactctgactcttctgtttgcttggcatgttgggaattcagagtggcgtttcgcaaaccgcactttagcttaggtggggttttgtgttgacttgtctacgtccacgttccttgtctgctgtttgcag

upper sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G303465_T04 (Zea mays), 5'ss of exon 1
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggatctctctctcttttcttttccttctatttctccgatgattgtgttttgggtta------------tttgattaaaaggatgaaatcttttccttctatttctc---------------
|||||||||||||  | ||||| || || |||||||||||||| || ||||| ||  | || ||||||||||||||||||||    ||| | ||||||||||| |  ||    |  | |       |      ||      ||  |  |  || |||| |              |||| || || | | || |  || |  |   | ||| |               
TCATGAAGAAGGCCGTCCCGGCCAACGGCAAGATCGCCAAGGACGCTAAGGAGACCCTGCAGGAGTGCGTCTCCGAGTTCATATCATTCGTGACCAGCGAgtaagttgacagttggcaccgcctggtagacggtagcgtagcgtagccttggtcttggatcgggttggtttttctttgttttaatgtaggataggttctgatgtaagttcacgggtgctggttgcag

upper sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G33550.2 (Glycine max), 5'ss of exon 2
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacg-cggatctctctctcttttcttttccttctatt--tctccgatgatt---gtgttttgggtta-------tttgattaaaaggatgaaatcttttc-cttctatttctc-------------------------------------------------------------------
|||||||||||||  ||||  | ||||| ||||| || |||||||| || |||||  | ||||| ||||| || || |||||||| ||||| ||||||||||  | | | | |      || | | | |||   |||   | ||  ||| ||   || |||| | | |       ||| | |  || | || | | ||||   || ||||| |                                                                    
TCATGAAGAAGGCTCTGCCTCCCAATGGCAAGATTGCGAAGGATGCAAAAGACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGAgtgagtcagttattagcaactatacatatccagttatcgatatcaaatgttttttgttttttagctcaaaatgttttttaatgtaaagctgcagttttttaatttttattttttggggattgggggttctgagaattttttaattactgaattccacgcacgtggttattatgacttgcag

upper sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT2G38880.7 (Arabidopsis thaliana), 5'ss of exon 2
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggatctctctctcttttcttttccttctatttctccgatgattgtgttttgggttatttgattaaaaggatgaaatcttttccttctatttctc-------
|||||||||| ||||||||  ||||||||||||| |  || ||||| ||||| || || || || |||||||| ||||||||||| |||||||| |||||||| ||   || |  | | | ||||||   |   |||| |  ||  ||    |||||   | |||| | ||||  ||  | || |||  |   | ||          
TCATGAAGAAAGCGTTGCCTCCTAATGGTAAGATTGGAAAAGATGCTAAGGATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgtatgcat-tcccaatttttcttctttcaatcgaatttgttggaaaat---attttg--ctctttggtgaaaaaaattga-tcatttgttggaactttgggtttgtg

upper sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EDP06643 (Chlamydomonas reinhardtii), 5'ss of exon 1
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcg-----gatctctctctcttttcttttccttctatttctccgatgattgtgtttt--gggttatttgattaaaaggatgaaatcttttccttctatttctc----------------------------------------------------
| |||||||||||| | |||   || |  || || ||||||||||| ||||| || ||||| ||||||||||| |||||||| || ||||||||    ||||| | |     |  | |   | || ||      |        | |||  |     |   |  ||     |||   |  | || |  ||   |  |    |     |                                                    
TTATGAAGAAGGCGCTCCCGAACAACGCGAAAATAGCCAAGGATGCAAAGGAGACGGTCCAGGAGTGCGTCTCGGAGTTCATTAGCTTCATCACGTCGGAgtaagtgtctgggggccccgccgctgtttggggacacggcccccgccgtcgcccccgccgtcaggagcccttgcccagcacgaagccatgcctcacgcacagcatgcatggatgtgcagcgtaaatgcattctatgctgatatggtttgcactatgtag

upper sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S25_10V6.1 (Physcomitrella patens), 5'ss of exon 1
----TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggatctctctctcttttcttt-tccttctatttctccgatgattgtgttttgggttatttgattaaaaggatgaaatcttttccttctatttctc
    ||||||||||||||||||| ||||||| |||||| ||||| ||||||||||| ||||| || ||||| || || || ||||||||||||||||| ||||||||  ||  | || |    | |   |  | ||   |||| | |   |||   | |         ||   |      ||    |  ||      |       
CGCATCATGAAGAAGGCGTTGCCTGCTAATGCTAAGATTGCCAAAGATGCGAAGGAGACTGTTCAGGAGTGTGTTTCAGAATTCATCAGTTTCATCACTAgcgagtatccgtttttcacaacgtctaaataattctgacatttttgcatagatcccgctgccctcatcttacctctgctaatcttgtagttgatccatgc-----

upper sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S25_89V6.1 (Physcomitrella patens), 5'ss of exon 2
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggatctctctctcttttcttttccttctatttc-tccgatgattgtgttttgggttatttgattaaaaggatgaaatcttttccttctatttctc
||||||||||||||||||| |||||||  ||||| ||||| ||||||||||| || || |||||||| || ||||| ||||||||||||||||| ||||||||  |   |   | |   |||||  |  | | | |  | |       |||| ||   | || |||   |      |||    | ||      || |    
TCATGAAGAAGGCGTTGCCTGCTAATGCCAAGATTGCCAAAGATGCGAAGGAGACAGTTCAAGAGTGTGTTTCCGAATTCATCAGTTTCATCACGAGCGAgtatccat-ttgatatggtttttcggtgtcatatgtcgcatgttgcccttgtcttactgtttctttacgtccgctaatgtggccgttggaccgtaataacg

upper sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ15374 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggatctctctctcttttcttttccttctatttctccgatgattgtgttttgggttatttgattaaaaggatgaaatcttttccttctatttctc
| |||||||||||| ||||||| ||||  ||||||||||||||||| ||||| || || ||||| |||||||| ||||||||||| |||||||| |||||||| |     || ||  || ||| |  |  |  ||  | ||   |  || |  ||||                                           
TAATGAAGAAGGCGCTGCCGGCGAATGCAAAGATCGCCAAGGATGCCAAGGAGACGGTGCAAGAATGCGTCTCGGAGTTCATCAGCTTCATCACTAGCGAgtaagtattgct-tcgatcctttgtggtgatgttaactatc---ttcttctactttgtag----------------------------------------

upper sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ24973 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggatctctctctcttttcttttccttctatttctccgatgattgtgttttgggttatttgattaaaaggatgaaatcttttccttctatttctc
| |||||||||||| ||||||| ||||  ||||||||||||||||| ||||| || || ||||| |||||||| ||||||||||| |||||||| |||||||| |     ||     |  ||||  | | || |        | ||||  | | ||    || ||                                   
TAATGAAGAAGGCGCTGCCGGCGAATGCAAAGATCGCCAAGGATGCCAAGGAGACGGTGCAAGAATGCGTCTCAGAGTTCATCAGCTTCATCACTAGCGAgtaagtattgctggaagttctttcgatcctttgt--------ggtgatactatcttcttctactttgcag------------------------------

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|110685257|gb|EE063468.1|EE063468
EST:     GACACTGTCCAATAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGA                         GGCTAGTGATAAGTGTCAGAAAGAGAAGCGAAAGACGATTAATGGTGATGA
genomic: GACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggat ... tcttgtttagGGCTAGTGATAAGTGTCAGAAAGAGAAGCGAAAGACGATTAATGGTGATGA
EST: gi|110690518|gb|EE067687.1|EE067687
EST:     GACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGA                         GGCTAGTGATAAGTGTCAGAAAGAGAAGCGAAAGACGATTAATGGTGATGA
genomic: GACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggat ... tcttgtttagGGCTAGTGATAAGTGTCAGAAAGAGAAGCGAAAGACGATTAATGGTGATGA
EST: gi|22014931|gb|BQ799965.1|BQ799965
EST:     GACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGA                         GGCTAGTGATAAGTGTCAGAAAGAGAAGCGAAAGACGATTAATGGTGATGA
genomic: GACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggat ... tcttgtttagGGCTAGTGATAAGTGTCAGAAAGAGAAGCGAAAGACGATTAATGGTGATGA
EST: gi|110425488|gb|EC991873.1|EC991873
EST:     CGAGTTCATCAGTTTCATCACCAGCGA                         GGCTAGTGATAAGTGTCAGAAAGAGAAGCGAAAGACGATTAATGGTGATGA
genomic: CGAGTTCATCAGTTTCATCACCAGCGAgtacgcggat ... tcttgtttagGGCTAGTGATAAGTGTCAGAAAGAGAAGCGAAAGACGATTAATGGTGATGA
EST: gi|110427866|gb|EC994320.1|EC994320
EST:     GACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGA                         GGCTAGTGATAAGTGTC
genomic: GACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggat ... tcttgtttagGGCTAGTGATAAGTGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggatctctctctcttttcttttccttctatttctccgatgattgtgttttgggttatttgattaaaaggatgaaatcttttccttctatttctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgaaa