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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttgattccaggttgtatttctatatatatgatcttcattctaaggtgcagtcatataaattgttaatgtgatgatttcag

Basic information

species Vitis vinifera
transcript Vv11s0016g04180.t01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 15
CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttgattccaggttgtatttctatatatatgatcttcattctaaggtgcagtcatataaattgttaatgtgatgatttcag---------
 |||||  | |||||||||||  | || || || |||||||| |||||||| ||||| || || || || ||||| || ||||||||||||||||| ||||||||       || | |  |   | |||| ||| |   | || |   |||||  ||    |  | |  | |   ||| |      ||            
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattgtgtgctccatgcaagaatttttattttgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacag

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 15
CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttgattccag------------gttgtatttctatatatatgatcttcattctaagg-tgcagtcatata---aattgttaatgtgatgatttcag
 ||||| || ||||||||||| ||||||||||| |||||||| |||||||| || || || ||||| || ||||| || || ||||||||||||||||||||| || | |||    || |             |||  | |||| |||||  |  ||||||   | |  | || |    ||   | || | |   | ||  || |||
TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgta-aatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacag

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GRMZM2G095348_T03 (Zea mays), 5'ss of exon 15
CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttgattcc---aggttgtatttctatatatatgatcttcatt---ctaaggtgc-agtcata---taaattgttaat---gtgatgatttcag---------
 || ||  | ||||||||||| ||||||||||| |||||||| |||||||| || || || ||||| |  ||||| || || ||||||||||||||||||||| || | |||  | |||   |    || ||  | | | || | |||  ||    | |   ||  |||||     | ||||||| |    || || |  |  |         
TCACGAGGTCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCGTTGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgta-aaaatagtctactccttgaaaacgttttcttctgtttaagttctctatatggccactttgtgagtcacgacttcaattgtttacacagttataagctttgtacttacag

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA13G43680.1 (Glycine max), 5'ss of exon 15
CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttga--ttccaggttgtatttctata-------tatatgatcttcatt--ctaaggtgcag---tcatataaattgttaatg--tgatgatttcag------
 |||||||| ||||| || |||||||| || || ||||||||||| ||||| || ||||| || ||||||||| ||||||| || ||||||||||||||||||| |     ||    ||| || ||     | || |       | |    ||||  ||   | |  | ||    ||||   |  | || |||  | ||||||          
ACATGAAATGAATGAACGTGTCAGAACAGGCATCTGGGTTGGGGATTGCTTTATCTACAACAATTCCTCTTGGAGACTTAATTACTGTGTTGGTGGTGAGgtattaactcttttcccttctagatttctagtttaaaaaagaattgtgcattcttttttaattgaactacaaggatcatgagacatcttgatgcataatgattatgaatttag

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 15
CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttga--ttccaggttgtatttctatatatatgatc-----ttcattctaa----ggtgcag---tcatataaattgttaatg--tgatgatttcag------
 |||||||| ||||| || ||||| || || || ||||||||||| ||||| || ||||| ||  |||||||| ||||||| || ||||||||||||||||||| |     ||    ||| || ||     | || | | |  ||      ||| || |||      | |     ||||   |  | || ||   | ||||||          
ACATGAAATGAATGAACGTGTCAGGACAGGCATCTGGGTTGGGGATTGCTTTATCTACAACAATACCTCTTGGAGACTTAATTACTGTGTTGGTGGTGAGgtattaactcttttcccttctagatttctagtttaaaaaaagaattgtgcattctttttaattgaactacgaggatcatgagacatcttgatacataatgattatgaatttag

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 15
CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttga--ttccaggttgtat----ttctatatatatgatcttcattctaaggtgcagtcatataaat-tgttaatgtgatgatttcag--------------------------------------------------------------
 |||||||| ||||| || ||||| || || || ||||||||||| || || || ||||| || || |||||| | ||||||||||||||||||||||||||||       ||    ||  || || ||      || |||| |||    |  | |||  | |    || | |   | |||| |||   |  ||  |                                                               
TCATGAAATGAATGAACGTGTCAGGACAGGGATCTGGGTTGGGGATTGTTTTATCTACAACAATTCTTCTTGGAGGCTTAACTATTGTGTTGGTGGTGAGgtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttag

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 4
CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttga--ttccaggtt----gtatttctatatatatgatcttcattctaaggtgcagtcatataaattgttaatgtgatgatttcag----------------------------------------------------------------
 |||||||| ||||| || ||||| || || || ||||||||||| || || || ||||  || || |||||| | ||||||||||||||||||||||||||||       ||    ||  || ||      |  ||| ||| |||    |  | |||  |      || | |   ||||     |||   | | |                                                                 
TCATGAAATGAATGAACGTGTCAGGACAGGGATCTGGGTTGGGGATTGTTTTATCTACAGCAATTCTTCTTGGAGGCTTAACTATTGTGTTGGTGGTGAGgtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttct-ttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttag

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 15
CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttgattccaggttgtatttctatatatatgatcttcattctaaggtgcagt-catataaattgttaatgtgatgatttcag
||| || |   |||| || || || || || ||||||||||||||||||||||||||||| ||||| ||||||   ||||||||||||||||| || ||||||    |||||  |||        ||||||||        ||| || || | || | || |  |||  |  || |||| |     |  |||
CCACGAGAATGATGAACGTGTTAGGACCGGTATATGGGTTGGGGACTGCTTCATTTACAACAACTCTTCTTGGAAGCTTAACTATTGTGTTGGAGGCGAGgtactcaagagtctatttt------tatttcta--------atcatctttatgagctacattatataatagctgctaatatacctgtggcag

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 15
CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttgattccaggttgtatttctatatatatgatcttcattctaaggtgcagtcatataa--attgttaatgtgatgatttcag
||||||||   |||| || || || || || ||||||||||| ||||| ||||||||||| ||||| || |||   |||||||| |||||||| || |||||||        ||  |  | ||||  || || |  || ||    |  || | |  || | ||  || |   ||| |||  |  | ||   ||
CCATGAAAATGATGAACGTGTTAGGACAGGTATATGGGTTGGTGACTGTTTCATTTACAACAACTCTTCCTGGAAGCTTAACTACTGTGTTGGAGGCGAGgtattg------tgcatatatgttg-gttactctg-atttggaagttgttatgaactggattctaatgatggttgctaacatcgtaatactag

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 5'ss of exon 15
CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttgattccaggttgtatt--tctata-tatatgatcttcattctaaggtgcagtcatataaatt---gttaatgtgatgatttcag-----
 || |||||   ||||||| | ||||||||  | |||||||| ||||||||||||||||| || ||  | ||| |||| ||||| ||||||||||| ||||||    |  ||    | || | || ||      ||  |  |   | | ||||  |      |||    || |||   | | ||| | |  || ||      
GCACGAAATTCCTGAGCGAATTAGAACTGGCTTGTGGGTTGGTGACTGCTTCATTTACAACAATTCAGCATGGAGACTCAACTACTGTGTTGGTGGAGAGgtaagtaatggtca--tacatgatggatcagctaatgctgcaccgtatccatttcagatactagtagattacattttagcttatgagttacttgcatccaat

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttgattccaggttgtatttctatatatatgatcttcattctaaggtgcagtcatataaattgttaatgtgatgatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG