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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAATGGGGCTTGTGGGTTGTCCACAAACTAGTGCTTACTGCTGTTTATGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgtctaatatatgccttgtctttgaagttgaatttgcctcatattgaagacctaatcactaaatttaagtctgtttcttctttcctttgatgcag

Basic information

species Vitis vinifera
transcript Vv14s0030g00750.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os03g54920.1 (Oryza sativa), 5'ss of exon 3
GTGAAATGGGGCTTGTGGGTTGTCCACAAACTAGTGCTTACTGCTGTTTATGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgtctaatatatgccttgtctttgaagttgaatttgcctcatattgaagacctaatcactaaatttaagtctgt-ttcttctttcctttgatgcag
| ||| |||||| | ||| || | |||||| | |||||||||| ||| |||||| | ||  |||||||||| |||||||  |||||||| |||||||||||| |  |||  ||  || | |           ||||   ||||  | |  |||      |  |  ||       | || |  || ||  ||  |||| |||||
GGGAAGTGGGGCCTATGGTTTCTACACAAATTGGTGCTTACTGGTGTCTATGGCCTGATTGTGTTCATGTATCACTCAAGGTGGAGAGACAGGTTACCTGgtaa--ttggttacaatttacagcac------agttatgtttgttt-aggttgtg----tgtttgctgttccataatcagcattttttattattttgttgcag

upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA19G42870.1 (Glycine max), 5'ss of exon 3
GTGAAATGGGGCTTGTGGGTTGTCCACAAACTAGTGCTTACTGCTGTTTATGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgtctaatatatgccttgtctttgaagttgaatttgcctcatattgaagacctaatcactaaatttaagtctgtttcttctttcctttgatgcag
| ||| |||  |||||||||||||||||| ||  |||| ||||||||||||||||||||| |||| |||||||| ||   ||||| ||| | ||| |||||||||    |  |      | ||  |   ||| |||    ||  || || ||      |||||  || |||||             |||| |||| ||||||
GGGAAGTGGAACTTGTGGGTTGTCCACAAGCTGTTGCTCACTGCTGTTTATGGCTTCATAATGTTTATGTACCATTCCGGATGGAAAGAAACGTTGCCTGgtgagccaattga---cgggactattacatgatgtt----ttaacttatttt------ctaattgcttaattt------------ccttttctttcatgcag

upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA03G40260.1 (Glycine max), 5'ss of exon 3
GTGAAATGGGGCTTGTGGGTTGTCCACAAACTAGTGCTTACTGCTGTTTATGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgtctaatatatgccttgtctttgaagttgaatttgcctcatattgaagacctaatcactaaatttaagtctgtttcttctttcctttgatgcag
| ||| |||  |||||||||||||||||| ||  |||| ||||||||||||||||||||| |||| || ||||| ||   ||||| ||| | ||| ||||||||| |  |  |    ||   |   |  ||   |||   || ||| || |      | |  |||   |                                 
GGGAAGTGGAACTTGTGGGTTGTCCACAAGCTGTTGCTCACTGCTGTTTATGGCTTCATAATGTTTATATACCATTCCGGATGGAAAGAAACGTTGCCTGgtgagttaattgacgggattattacacgatgt--ttgtgattacctaatttcctcttctt--tcatgcag--------------------------------

upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G37380.1 (Glycine max), 5'ss of exon 3
GTGAAATGGGGCTTGTGGGTTGTCCACAAACTAGTGCTTACTGCTGTTTATGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgtctaatatatgccttgtctttgaagttgaatttgcctcatattgaagacctaatcactaaatttaagtctgtttcttctttcctttgatgcag
||||| |||  ||||||||||| |||||| ||  |||||||   ||||||||| ||||||||||||||||| || || |  |||||||| |||||||||||| || | ||    |  ||   || | ||  |  || |||| || | ||   ||   | ||||                  ||||  |  |||||  | |||
GTGAAGTGGAACTTGTGGGTTGCCCACAAGCTGTTGCTTACCCTTGTTTATGGTTTCATATTGTTCATGTATCATTCTAGGTGGAGAGAAAGGTTACCTGgtaagttagttgcctggat-tgttatattgcatctttaattagctttat---gataccataat------------------ttctcttccccttttttacag

upper sequence: Vv14s0030g00750.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G05010.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGAAATGGGGCTTGTGGGTTGTCCACAAACTAGTGCTTACTGCTGTTTATGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgtctaatatatgccttgtctttgaagttgaatttgcctcatattgaagaccta-----atcactaaatttaagtctgtttcttctttcctttgatgcag
 | ||||||||||| |||||  ||||||| ||  | ||  |||   |||||||  | ||||| ||||||||| |||| |||||||||||||| ||||| |||||     || |  |      |  || ||   |||| ||  |||      ||   ||        || ||| |    |  | | ||| || |    |||||     
TTCAAATGGGGCTTATGGGTCATCCACAAGCTCTTACTAGCTGGCATTTATGGGATGATATTCTTCATGTACAACTCCAAATGGAGAGAGAGATTACCAGgtgaatacatcgaccactcatatcctccttatggttgcataagccaatagctgttcactggcttctattactcatcccatatgtttttattttccggtttgacag--

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|30131882|gb|CB917221.1|CB917221
EST:     TGGCTTCATATTGTTCATGTACCACTCACAATGGAGAGAGAGGTTACCTG                         CAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAATGCAT
genomic: TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgt ... tttgatgcagCAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAATGCAT
EST: gi|22012612|gb|BQ797646.1|BQ797646
EST:     TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGCTACCTG                         CAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAATGCAT
genomic: TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgt ... tttgatgcagCAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAATGCAT
EST: gi|110366928|gb|EC930848.1|EC930848
EST:     TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTG                         CAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAATG
genomic: TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgt ... tttgatgcagCAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAATG
EST: gi|110365218|gb|EC927851.1|EC927851
EST:     TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTG                         CAAGACCTGCATTATACAAATATATCACAATCATGTGCTGCTTGAATGCAT
genomic: TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgt ... tttgatgcagCAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAATGCAT
EST: gi|30133320|gb|CB918659.1|CB918659
EST:     TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGCTACCTG                         CAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAATGCAT
genomic: TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgt ... tttgatgcagCAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAATGCAT
EST: gi|110380174|gb|EC945419.1|EC945419
EST:     TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTG                         CAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAAT
genomic: TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgt ... tttgatgcagCAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAAT
EST: gi|110703012|gb|EE079484.1|EE079484
EST:     TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGCTACCTG                         CAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAATGCAT
genomic: TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgt ... tttgatgcagCAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAATGCAT
EST: gi|110394639|gb|EC959842.1|EC959842
EST:     TGGCTTCATATTGTTCATGTCCCACTCAAAATGGAGAGAGAGGTTACCTG                         CAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAATGCAT
genomic: TGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgt ... tttgatgcagCAAGACCTGCATTCTACAAATATATCACAATCATGTGCTGCTTGAATGCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAAATGGGGCTTGTGGGTTGTCCACAAACTAGTGCTTACTGCTGTTTATGGCTTCATATTGTTCATGTACCACTCAAAATGGAGAGAGAGGTTACCTGgtgagattgtctaatatatgccttgtctttgaagttgaatttgcctcatattgaagacctaatcactaaatttaagtctgtttcttctttcctttgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG