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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGTTGCTGGATCTCAACCAATGAATGCTATTGCATTTGTTATTGATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattctgtgtatatgattataaatttttcattcttccacatcttctttcttaacttgctgtttgtgacgagcag

Basic information

species Vitis vinifera
transcript Vv08s0058g00510.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0058g00510.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os12g01580.1 (Oryza sativa), 5'ss of exon 10
TTTGTTGCTGGATCTCAACCAATGAATGCTATTGCATTTGTTATTGATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtacca--ttctgtgtatatgat-------tata-aatttttcattctt--ccacatcttctttcttaacttgctgtttgtgacgag-cag
|||||  |||  ||||||||||| |||||| |||| ||||| || ||||| ||||||||||| ||||| |||||||  |  |  || ||||| |  || |    |||| |   ||| ||       | || | ||| ||| |  |  |  || | || |  | |  ||  | ||| |   |   |||
TTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACAgttcagatttctattcttatcatgtcccattgtatagtttatcagttatagctgcagcatcctaatcacattagtatttttcttgtttcag

upper sequence: Vv08s0058g00510.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM5G890665_T01 (Zea mays), 5'ss of exon 10
TTTGTTGCTGGATCTCAACCAATGAATGCTATTGCATTTGTTATTGATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattctgtg--tatatgattataaatttttcattcttccacatcttctttc-ttaacttgctgtttgtgacgagcag----------------------------------------------
|||||  |    ||||| ||  |||||||||||||||| ||   |||||| ||||||||||| ||||| |||||||  |||||||| || |||| ||| |   |   |     ||   |     ||| ||   ||  | | |   ||   | ||| | ||   |   | |  |                                                  
TTTGTCACCATTTCTCAGCCGGTGAATGCTATTGCATTCGTGGCTGATGGGCTCTACTATGGTGTTTCTGACTTTGCCTATGCTGCATATTCCACGgttctgattcataatcctactctgtcgcattattatgtcaacgatactatcacacattatcatgtcatcaattatcacttcaacacaactttgccatcctaatcgtgtcaaatctttgttgtttcag

upper sequence: Vv08s0058g00510.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA07G19210.1 (Glycine max), 5'ss of exon 14
TTTGTTGCTGGATCTCAACCAATGAATGCTATTGCATTTGTTATTGATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattctgtgtatatgattataa-atttttcattcttccacatcttctttcttaacttgctgtttgtgacgagcag-------------------------------
||||||||||||||||||||| |||||||| | |||||||||||||||||  | || |||||||| |||||||||||||||||||| ||||| ||||||   | ||      ||| ||  || ||  || |   ||||| ||  | ||||     |  ||  || |  || ||                                 
TTTGTTGCTGGATCTCAACCAGTGAATGCTTTGGCATTTGTTATTGATGGGATTTATTATGGGGTATCAGACTTTGGATATGCTGCTTACTCGATGgtaagttcctaca---atggttgaaagatagttaaacattccatattatttttccctcttaactcattatttcgtgctcttttttttcttttggcttttgttatgggtag

upper sequence: Vv08s0058g00510.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA18G43740.1 (Glycine max), 5'ss of exon 14
TTTGTTGCTGGATCTCAACCAATGAATGCTATTGCATTTGTTATTGATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattctgtgtatatgatt-ataaatttttcattcttccacat----cttctttcttaacttgctgt-ttgtgacgagcag------------------------------
            ||||||||| |||||||| | |||||||||||||||||  | || || ||||| ||||||||||| |||||||| ||||| ||||||   | ||      ||| || | | ||  || |   | ||| ||    |||   ||||||||   |   | ||| |                                    
------------TCTCAACCAGTGAATGCTTTGGCATTTGTTATTGATGGGATTTATTACGGGGTATCAGACTTTGGTTATGCTGCTTACTCGATGGTAATTTCCTAC---CATGgttgaaagatagttaaacatgccatatgattctttcctcttaactcatttcctcgtgccctttttttcttttggtttttgttatggtggtgttag

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|32249157|gb|CD714976.1|CD714976
EST:     ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATG                         GTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
genomic: ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattct ... tgacgagcagGTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
EST: gi|32267493|gb|CD716456.1|CD716456
EST:     ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATG                         GTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
genomic: ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattct ... tgacgagcagGTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
EST: gi|32271344|gb|CD720503.1|CD720503
EST:     ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATG                         GTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
genomic: ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattct ... tgacgagcagGTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
EST: gi|30327458|gb|CD010720.1|CD010720
EST:     ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATG                         GTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
genomic: ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattct ... tgacgagcagGTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
EST: gi|32248530|gb|CD714349.1|CD714349
EST:     ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATG                         GTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
genomic: ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattct ... tgacgagcagGTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
EST: gi|161714495|gb|FC064464.1|FC064464
EST:     ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATG                         GTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
genomic: ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattct ... tgacgagcagGTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
EST: gi|32247951|gb|CD713770.1|CD713770
EST:     ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATG                         GTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
genomic: ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattct ... tgacgagcagGTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
EST: gi|32269980|gb|CD719139.1|CD719139
EST:     ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATG                         GTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
genomic: ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattct ... tgacgagcagGTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
EST: gi|32248555|gb|CD714374.1|CD714374
EST:     ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATG                         GTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA
genomic: ATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattct ... tgacgagcagGTATTAGTTGCACTAATATCTTCAGTGTTCCTGTTGCTGGCTGCTCCTGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGTTGCTGGATCTCAACCAATGAATGCTATTGCATTTGTTATTGATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATGgtaccattctgtgtatatgattataaatttttcattcttccacatcttctttcttaacttgctgtttgtgacgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC