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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCGTGGCACTTCTTTATGCTTCCAAAGAGTTGGACAAACTGCCAACATCAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttagtattcattcattttctaatatttaaaagacattcctcagcttggattagtctgtaaataattcttgtggaatcacacaagagtcattcaggatag...

Basic information

species Vitis vinifera
transcript Vv05s0051g00340.t01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 15
TGGCGTGGCACTTCTTTATGCTTCCAAAGAGTTGGACAAACTGCCAACATCAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttag-------tattcattcattttctaatatttaaaagacattcctcagcttggattag--tctgtaaataattcttgtggaatcacacaagagtcattcaggatag
 || || |||||||||||||| || || ||| |||| ||| |||| ||  | ||||||||||| ||||||||||| || || || ||||||||| |||| ||| |       || | | |  |  | |  | |||    ||  || ||   || |||  |    |||   | || |  | | | |                        
AGGTGTTGCACTTCTTTATGCATCAAAGGAGCTGGATAAATTGCCGACTGCTAACTTTGATCAAAAGATTGGTGTACAAATCATTCAGAATGCTTTGAAGgtttgggagggataataacttctcatttcctgttttgctga--tttcttctctgggagcaaaacctgatgacaacttattttgcag-----------------------

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 14
TGGCGTGGCACTTCTTTATGCTTCCAAAGAGTTGGACAAACTGCCAACATCAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttagtattcattcattttctaatatttaaaagacattcctcagcttggattagtctgtaaataattcttgtggaatcacacaagagtcattcaggatag
||| || || ||||| ||||| || || ||| | || ||  |||  ||| |||| |||||||||||||||||||| || || || ||||||||| |||| ||  |     |   || ||  | | |||     | |||| |     ||   ||  |||      | | || || |  ||                     
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggagaaga-atgttggattttttcccccagattcatacttgtgtgctaagctggcgtggaatattttgtatgcag--------------------

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 13
TGGCGTGGCACTTCTTTATGCTTCCAAAGAGTTGGACAAACTGCCAACATCAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttagtattcattcattttctaatatttaaaagacattcctcagcttggattagtctgtaaataattcttgtggaatcacacaagagtcattcaggatag
 || ||||| ||||| || ||  | | ||||||||| ||||| |||||| | |||||||| |||||||||||||| |||||||| ||||| ||  |||| |||        |  ||| | ||  | | |||      ||||| | |  ||| | |   | |  |    ||||   | |        ||    |||     
AGGTGTGGCTCTTCTATACGCAGCAAGAGAGTTGGAAAAACTTCCAACAGCCAACTTTGACCAGAAGATTGGTGTCCAGATTATTCAGAACGCATTGAAGgttt-------tctattctttagaactaaaa------tcctctgatctgat-aattgatgacaagaaattgttttaacgagttttggtttaccag-----

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|34547889|gb|CF516121.1|CF516121
EST:     CAAATTTTGATCAGAAGATTGGTGTTCAGATTATTCAGAATGCTCTGAAA                         ACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
genomic: CAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttagtattc ... ttatatgcagACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
EST: gi|34542276|gb|CF510508.1|CF510508
EST:     CAAATTTTGATCAGAAGATTGGTGTTCAGATTATTCAGAATGCTCTGAAA                         ACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
genomic: CAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttagtattc ... ttatatgcagACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
EST: gi|33404079|gb|CF209706.1|CF209706
EST:     CAAATTTTGATCAGAAGATTGGTGTTCAGATTATTCAGAATGCTCTGAAA                         ACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
genomic: CAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttagtattc ... ttatatgcagACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
EST: gi|352785457|gb|FQ477671.1|FQ477671
EST:     CAAATTTTGATCAGAAGATTGGTGTTCAGATTATTCAGAATGCTCTGAAA                         ACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
genomic: CAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttagtattc ... ttatatgcagACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
EST: gi|110363713|gb|EC927323.1|EC927323
EST:     CAAATTTTGATCAGAAGATTGGTGTTCAGATTATTCAGAATGCTCTGAAA                         ACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
genomic: CAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttagtattc ... ttatatgcagACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
EST: gi|110700181|gb|EE077929.1|EE077929
EST:     CAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAA                         ACGCCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAAGGGGCTGTTGTG
genomic: CAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttagtattc ... ttatatgcagACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
EST: gi|77587495|gb|DV222914.1|DV222914
EST:     CAAATTTTGATCAGAAGATTGGTGTTCAGATTATTCAGAATGCTCTGAAA                         ACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
genomic: CAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttagtattc ... ttatatgcagACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
EST: gi|34547812|gb|CF516044.1|CF516044
EST:     CAAATTTTGATCAGAAGATTGGTGTTCAGATTATTCAGAATGCTCTGAAA                         ACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG
genomic: CAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttagtattc ... ttatatgcagACACCTGTGTTCACAATTGCTTCTAATGCTGGAGTTGAGGGGGCTGTTGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCGTGGCACTTCTTTATGCTTCCAAAGAGTTGGACAAACTGCCAACATCAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttagtattcattcattttctaatatttaaaagacattcctcagcttggattagtctgtaaataattcttgtggaatcacacaagagtcattcaggatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caggata