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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATAAACCAATCAAAGGTTCTACAAACAACCATAAAAAGTTGGGCAATGCTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgccacttcattcaattttgtgtttcctttaccattcttttatgactagtatttgtttctcaattttcggaactatgagtgaatgctatcgct...

Basic information

species Vitis vinifera
transcript Vv18s0076g00260.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 5'ss of exon 9
TGATAAACCAATCAAAGGTTCTACAAACAACCATAAAAAGTTGGGCAATGCTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgccac-ttcattcaattttgtgtttcctttaccattcttttatga-ctagtatttgtttc--tcaattttcggaactatgagtgaatgctatcgct
   | || |     |||   |  | ||  |||| || |  |||||    || || |||||||| |||||||| ||||| |||| ||| |||||||||||||| ||||  | |  |    | ||  || |   |  || |  | | |||| | | |||| |  |   ||   |||| ||   |   |  ||  ||||  ||    
CAGTGAAGCGCCACAAGAACCAGCTAAACACCACAATAGATTGGGACCAGCAGGCCTTGCATTGCATTATGCAAATATCATCAATCAGATTGATACTCTTgtaagttcacaaaatctgcttaacattctaaatttttaattactattttgtcatctagaagataaatcaaccaatatttcaa--caccagc-aatgtcatgag-

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G046846_T01 (Zea mays), 5'ss of exon 9
TGATAAACCAATCAAAGGTTCTACAAACAACCATAAAAAGTTGGGCAATGCTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttg---------ccacttcattcaattttgtgtttcctttaccattcttttatgactagtatttgtttctcaattttcggaactatg--agtgaatgctatcgct-----------------------------------------------------------------------------------
   | ||  |    | |   |||| ||    | ||| |  |||||    || ||||||||| | |||||||| ||||| |||| ||| |||||||||||||| ||||           |   |  |||   || | ||| ||||  |  || |   ||| |  |||  |||     || ||   ||   | |   |||   |      ||                                                                                    
CAGTGAAGAATCACAGGAACCTACCAAACGACGTAATAGATTGGGTCCAGCAGGTCTTGCACTGCATTATGCAAATATCATCAGTCAGATTGATACTCTTgtaagttcacaggatccactgttctattgttttctctgtgtcctgcattatgcaaatatcatcagt--ttgacctacagttcatggggttgtactagtagttttgtgtgccacacaaattgaatttgttgtgctaagaaaatcattttttttgtttcttttctggtagcctaacaagggttgatcaattgacag

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA20G31400.1 (Glycine max), 5'ss of exon 11
TGATAAACCAATCAAAGGTTCTACAAACAACCATAAAAAGTTGGGCAATGCTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgccacttcattcaattt--tgtgtttcctttaccattctttt--atgactagtatttgtttctcaattttcggaac-tatgagtgaatgctatcgct
|||||| |||   |||| ||||  |  ||||||||| ||||||||   |||||||||||| || ||||||||||| |||||||||||||||||||||||||||||||    | || | |  | |   | |      ||||  ||| | ||  |||   |   | ||||  ||  | || |  |  ||  | ||  |  ||     
TGATAAGCCAGCGAAAGATTCTCAAGGCAACCATAAGAAGTTGGGGTCTGCTGGTCTTGCTTTGCATTATGCGAACATTATCACTCAAATTGATACTCTTgtgagttaaggattttacttgaataaatctacaatatttattattgtcttggatgttcaaattatgttagtctctgtttgtcatgtaatattgtttctta-----

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA10G36210.1 (Glycine max), 5'ss of exon 11
TGATAAACCAATCAAAGGTTCTACAAACAACCATAAAAAGTTGGGCAATGCTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgccacttcattcaattttgtgtttcctttaccattcttttatgact-agtatttgtttctcaattttcggaactatgagt-gaatgctatcgct
|||||| | |   |||| ||||  |  ||||||||| ||||||||   |||||||||||| || ||||||||||| ||||||||||||||||||||||| ||||||||   | || | | || ||    |   || ||  |||  ||  || || || | ||  |  |   |||| |   || |  || |  ||   | |  
TGATAAGCAAGCGAAAGATTCTCAAGGCAACCATAAGAAGTTGGGATCTGCTGGTCTTGCTTTGCATTATGCGAACATTATCACTCAAATTGATACTCTCgtgagtttaggattttacttaaatt-acataatctctattatttgttactgtcttagaagttcatattatcttttagtctctgttggttgtgtgactttgt-

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT1G34320.1 (Arabidopsis thaliana), 5'ss of exon 9
TGATAAACCAATCAAAGGTTCTACAAACAACCATAAAAAGTTGGGCAATGCTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgccacttcattcaattttgtgtttcctttaccattcttttatgactagtatttgtttctcaattttcggaactatgagtgaatgctatcgct-
|||||| ||    || |   |  ||| ||| ||||||||  |||||  |||||||||||| || ||||| || || || || |||||||||||||||||||| ||| |   | |   ||  ||    |  ||    |  || | |||      | ||       |||   ||   || | | | | |   |  | || |  
TGATAAGCCTGCAAATGACCCGCCAATCAATCATAAAAAACTGGGCTCTGCTGGTCTTGCCTTGCATTACGCAAACATCATTACTCAAATTGATACTCTTgtaagtatattattcttttttatcacttagttttactttcaatgtttggcctgttgt-ccaaactctaggttcctgggattgtaaatcgtttgtttctcgt

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|110719053|gb|EE096590.1|EE096590
EST:     CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTT                         GTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
genomic: CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgc ... acataatcagGTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
EST: gi|110720867|gb|EE097166.1|EE097166
EST:     CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTT                         GTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
genomic: CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgc ... acataatcagGTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
EST: gi|110720638|gb|EE096734.1|EE096734
EST:     CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTT                         GTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
genomic: CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgc ... acataatcagGTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
EST: gi|110718519|gb|EE095448.1|EE095448
EST:     CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTT                         GTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
genomic: CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgc ... acataatcagGTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
EST: gi|110720216|gb|EE095942.1|EE095942
EST:     CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTT                         GTGTCCCGATCAAGTTCTGTGCCTCCACATATGAGGGATGCCTTATACCAA
genomic: CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgc ... acataatcagGTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
EST: gi|110720676|gb|EE096807.1|EE096807
EST:     CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAGTTGATACTCTT                         GTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
genomic: CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgc ... acataatcagGTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
EST: gi|110720592|gb|EE096647.1|EE096647
EST:     CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTT                         GTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
genomic: CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgc ... acataatcagGTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
EST: gi|110719214|gb|EE096935.1|EE096935
EST:     CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTT                         GTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATATCAA
genomic: CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgc ... acataatcagGTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
EST: gi|110713860|gb|EE090149.1|EE090149
EST:     CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTT                         GTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
genomic: CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgc ... acataatcagGTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
EST: gi|110718805|gb|EE096054.1|EE096054
EST:     CTGGTCTTACATTACATTATGCGAATATTATCACTCAAATTGATACTCTT                         GTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
genomic: CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgc ... acataatcagGTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
EST: gi|110719766|gb|EE095191.1|EE095191
EST:     CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTT                         GTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
genomic: CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgc ... acataatcagGTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
EST: gi|110720643|gb|EE096746.1|EE096746
EST:     CTGGTCTTGCATTACATTATGCGGATATTATCACTCAAATTGATACTCTT                         GTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA
genomic: CTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgc ... acataatcagGTGTCCCGATCAAGTTCTGTGCCTCCAAATATGAGGGATGCCTTATACCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATAAACCAATCAAAGGTTCTACAAACAACCATAAAAAGTTGGGCAATGCTGGTCTTGCATTACATTATGCGAATATTATCACTCAAATTGATACTCTTgtgagtttgccacttcattcaattttgtgtttcctttaccattcttttatgactagtatttgtttctcaattttcggaactatgagtgaatgctatcgct

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