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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGATAAGGAAGCCAGAACAGCTGGAGCAAGTGGGCTCCCTTATCATCCCTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccactttctctatttcttcatatatttatatttgtttaattcggattatgggtaccgatgaggaccggaagaacatattccttatttatttatt...

Basic information

species Vitis vinifera
transcript Vv06s0004g03000.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03000.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os02g03740.1 (Oryza sativa), 5'ss of exon 2
GGAGATAAGGAAGCCAGAACAGCTGGAGCAAGTGGGCTCCCTTATCATCCCTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccactttctctatttcttcatatatttatatttgtttaattcggattatgggta-ccgatgaggaccggaag-aacatattccttatttatttatt
|||| |  ||||||| || |||||| ||    | | ||| || |||||||| || || |||||||||||||||||||| |||||  | ||||||||||||||    || |    |||  || |   |    || | |   ||||   |  || ||  ||| | | | |  |  ||||   |     | | |   | |  |  
GGAGGTGCGGAAGCCGGAGCAGCTGCAGGGGCTCGACTCGCTCATCATCCCCGGCGGCGAGAGCACCACCATGGCCAAACTCGCCAACTACCACAACCTGgtaactccccccattcttcttttggttgctgttctttcgttttag--caaatcatttgtatctgtttattattggaattgatgcgatgcatgaatctccacg

upper sequence: Vv06s0004g03000.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G023528_T02 (Zea mays), 5'ss of exon 2
GGAGATAAGGAAGCCAGAACAGCTGGAGCAAGTGGGCTCCCTTATCATCCCTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtct-----tcccactttctctatttcttcatatattt-atatttgtttaattcggattatgggtaccgatgaggaccggaagaacatattccttatttatttatt
     |  | |||||||| |||||        | | ||| || |||||||| ||||| ||||||||||||||||||||||||||  | |||||||| |||||       |||  |||  ||| | ||| |   | |    |    |     |  | |     |   ||  |   | |   | |        |    ||  |     
----GTGCGCAAGCCAGAGCAGCTCCTCGGCATCGACTCGCTCATCATCCCCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTGGTGGgtgggtccttcttcttctttgtctccgcttctcccgtggccgacgcctctgcagggcagcctcccctccaggctctagggctgccaccacccttgttgcg--

upper sequence: Vv06s0004g03000.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G023528_T03 (Zea mays), 5'ss of exon 2
GGAGATAAGGAAGCCAGAACAGCTGGAGCAAGTGGGCTCCCTTATCATCCCTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtct-----tcccactttctctatttcttcatatattt-atatttgtttaattcggattatgggtaccgatgaggaccggaagaacatattccttatttatttatt
|||| |  | |||||||| |||||        | | ||| || |||||||| ||||| ||||||||||||||||||||||||||  | |||||||| |||||       |||  |||  ||| | ||| |   | |    |    |     |  | |     |   ||  |   | |   | |        ||    || |     
GGAGGTGCGCAAGCCAGAGCAGCTCCTCGGCATCGACTCGCTCATCATCCCCGGTGGCGAGAGCACCACCATGGCCAAGCTCGCCAACTACCACAATCTGgtgggtgggtccttcttcttctttgtctccgcttctcccgtggccgacgcctctgcagggcagcctcccctccaggctctagggctgc-caccacccttgt-----

upper sequence: Vv06s0004g03000.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA03G08260.2 (Glycine max), 5'ss of exon 2
GGAGATAAGGAAGCCAGAACAGCTGGAGCAAGTGGGCTCCCTTATCATCCCTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtc-------ttcccactttc---tctatttcttcatatatttatatttgtttaattcggattatgggtaccgatgaggaccggaagaacatattccttatttatttatt
||||||  | |||||||| |||||  |   | |  | ||||| || |||||||||||||| |||||||||||||| |||||||| || || ||||||||||||       || || ||||    | ||||| |  || |||| |||||||  ||    | |  ||   | ||  | |    |||||    |||||       |       
GGAGATTCGAAAGCCAGAGCAGCTTAACACAATTAGTTCCCTCATTATCCCTGGTGGAGAAAGCACCACCATGGCTAAGCTCGCCGAGTATCACAACCTGgtcgctttctttacctcttttgtttttatttttatatctattcatatttgcgtagactgaaaaatatttgcctttta---tcggaaaggaatatttaaagggt-------

upper sequence: Vv06s0004g03000.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT5G60540.1 (Arabidopsis thaliana), 5'ss of exon 1
GGAGATAAGGAAGCCAGAACAGCTGGAGCAAGTGGGCTCCCTTATCATCCCTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccactttctctatttcttcatatatttatatttgtttaattcggattatgggtaccgatgaggaccggaagaacatattccttatttatttatt---------
 ||||| |||||| | || |||||       ||    || |||||||| ||||| || |||||||||||||||||||| ||||| || || || ||| |||||  | | || ||||| |    ||  |  ||  | ||||       |   ||   |  ||   | |        |       ||  |||| | | | ||         
CGAGATTAGGAAGGCTGACCAGCTTCTCACCGTTTCTTCTCTTATCATTCCTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctc-ctctctctctagaatctaaagttattgtttgcgaggacccacttgaagaaactagtta--------aaggttccttttttatgtgtgttttgacacgaat

upper sequence: Vv06s0004g03000.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S33_212V6.2 (Physcomitrella patens), 5'ss of exon 2
GGAGATAAGGAAGCCAGAACAGCTGGAGCAAGTGGGCTCCCTTATCATCCCTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccactttctctatttcttcatatatttatatttgtttaattcg-gattatgggtaccgatgaggaccggaagaacatattccttatttatttatt---------------------------------------------------------------------
|||  || | ||||  || ||  ||| |    ||  |    | || || |||||||| ||||||||||||||||||||||| || ||  |  ||||||| ||      |  ||      ||| |  | | | | |   | ||     || ||    |  |  |     | |      | || | ||| |  ||| | | ||                                                                     
GGAAGTACGCAAGCTGGAGCAATTGGTGGGGTTGTCCGGTTTGATTATTCCTGGTGGCGAGAGCACCACCATGGCCAAGCTGGCGGAGAAGAACAACCTTgttagtggaaatttatctcttccttttgtttctgtgcctcttcctcccgcgaactcgaatcgcctcacgaaaatagtggactttttcttggtttttatttttatttttaaattgtactttttcttgtgcaccaaataaacgctgacgtcgattgtaaaaccctgtcgcag

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|352794338|gb|FQ481569.1|FQ481569
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|351032258|gb|FQ460515.1|FQ460515
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|352799005|gb|FQ480854.1|FQ480854
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|349829976|gb|FQ420236.1|FQ420236
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|351027188|gb|FQ440056.1|FQ440056
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|352790573|gb|FQ478212.1|FQ478212
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|351039932|gb|FQ464970.1|FQ464970
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|122689691|gb|EC942857.1|EC942857
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|351038808|gb|FQ464674.1|FQ464674
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|349814306|gb|FQ398746.1|FQ398746
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|351039369|gb|FQ461236.1|FQ461236
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|349824064|gb|FQ417451.1|FQ417451
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|351036688|gb|FQ457401.1|FQ457401
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|349815212|gb|FQ400367.1|FQ400367
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|351046692|gb|FQ453308.1|FQ453308
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|351041568|gb|FQ455784.1|FQ455784
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|351037793|gb|FQ464234.1|FQ464234
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|349828753|gb|FQ418488.1|FQ418488
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
EST: gi|351033877|gb|FQ462286.1|FQ462286
EST:     CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTG                         TTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC
genomic: CTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccac ... ttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGATAAGGAAGCCAGAACAGCTGGAGCAAGTGGGCTCCCTTATCATCCCTGGTGGAGAGAGCACCACCATGGCCAAGCTCGCTGAATACCACAACCTGgtcttcccactttctctatttcttcatatatttatatttgtttaattcggattatgggtaccgatgaggaccggaagaacatattccttatttatttatt

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaagaa