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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCTAATGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTCATATTGTATGAAGAAGAAATTGCGgtaaacattcattgatcgatcaaaaagtggcatgcatcacccaattatttattttctcagatgaattttgtgcctggctattag

Basic information

species Vitis vinifera
transcript Vv18s0001g14680.t01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g14680.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 18
GCTGCTAATGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTCATATTGTATGAAGAAGAAATTGCGgtaaa---cattcattgatcgatcaaaaagtggcatgcatcacccaattattt-------attttctcagatgaattttgtgcctggctattag--------------------------------------------------------------------------------------------
|| || ||||| |||||||| || || ||||||||||| || || ||||| |||||||| || ||||||||||||||||||||| |   | | | |||  |   |               |   |  |||| ||        || | | | || |    ||   |     || |                                                                                             
GCGGCCAATGATTGTGATCTGGAACCGGTTGCTTATGAGTTCTTTACTCAAGCATTCATCTTATATGAAGAAGAAATTGCGgtataagccctgcgttgcccttccttgtgcacatccattttgtcacattacttcaattgagttatttgatataacccctggatcatatcataaacacatgcaatatgcattccaacactagggtcaatagctcattttataactctatacgattttcgacctacaatgtttgcatgctacatgcag

upper sequence: Vv18s0001g14680.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM5G825524_T01 (Zea mays), 5'ss of exon 18
GCTGCTAATGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTCATATTGTATGAAGAAGAAATTGCGgta--aacattcattgatcgatcaaaaagtggcatgcatcacccaatt-atttattttctcagatgaattttg-tgcctg--gctattag---------------------------------------------------------------------------------------------------
||||| |||||||||||| | || || ||||||||||| || || ||||| || |||||||| |||||||||||||||||||||  |||  ||     ||  ||      || | |    ||   ||    |  | || |   |   ||||  | ||  ||  || ||  |                                                                                                   
GCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATATTATATGAAGAAGAAATTGCGgtatgaaccctcccatctccttccctgtatgccctagtgcatgtaacccgtgcacttccagtgcctaattgagctgtttgatgcaatctggactgtatcataatgtatgctatatgcctttgtaaggacattttgttgcatttacatttggtctattttctctttacaatatttctgttccacaagcag

upper sequence: Vv18s0001g14680.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM5G825524_T02 (Zea mays), 5'ss of exon 18
GCTGCTAATGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTCATATTGTATGAAGAAGAAATTGCGgta--aacattcattgatcgatcaaaaagtggcatgcatcacccaatt-atttattttctcagatgaattttg-tgcctg--gctattag---------------------------------------------------------------------------------------------------
                            |||||||||| || || ||||| || |||||||| |||||||||||||||||||||  |||  ||     ||  ||      || | |    ||   ||    |  | || |   |   ||||  | ||  ||  || ||  |                                                                                                   
----------------------------TTGCTTATGAGTTCTTTACTCAAGCGTTCATATTATATGAAGAAGAAATTGCGgtatgaaccctcccatctccttccctgtatgccctagtgcatgtaacccgtgcacttccagtgcctaattgagctgtttgatgcaatctggactgtatcataatgtatgctatatgcctttgtaaggacattttgttgcatttacatttggtctattttctctttacaatatttctgttccacaagcag

upper sequence: Vv18s0001g14680.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 19
GCTGCTAATGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTCATATTGTATGAAGAAGAAATTGCGgtaaaca-------------ttcattgatcgatcaaa---aagtgg--catgcatcacc--caattatttattttctcagatgaattttgtgcctggctattag------------------------------------------------------------------------------
||||| |||||||||||| | || || ||||||||||| || || ||||| || ||||| || ||||||||||||||  |||||   |             |||  ||   |  |||    | |||   ||||||   ||   |  || ||    | |  |||| |   ||  |      || |                                                                               
GCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACGgtatgaaccttcccatccccttccctgtatgtccaagtgcatgtgacccatgcacttccagtacctaattgagctgttcgatgtaacctggactgtatcataatgtatgctatatgcctttgtaaggacatcgtttacatttggtctattttctctctatgatgtttctgttccacaagcag

upper sequence: Vv18s0001g14680.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM5G844195_T04 (Zea mays), 5'ss of exon 1
-------------------GCTGCTAATGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTCATATTGTATGAAGAAGAAATTGCGgtaaaca-------------ttcattgatcgatcaaa---aagtggc--atgcatcacc--caattatttattttctcagatgaattttgtgcctggctattag------------------------------------------------------------------------------
                   ||||| |||||||||||| | || || ||||||||||| || || ||||| || ||||| || ||||||||||||||  |||||   |             |||  ||   |  |||    | ||| |  |||||   ||   |  || ||    | |  |||| |   ||  |      || |                                                                               
GATTATGTTTTTAATTTAGGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACGgtatgaaccttcccatccccttccctgtatgtccaagtgcatgtgacccatgcacttccagtacctaattgagctgttcgatgtaacctggactgtatcataatgtatgctatatgcctttgtaaggacatcgtttacatttggtctattttctctctatgatgtttctgttccacaagcag

upper sequence: Vv18s0001g14680.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA17G37870.1 (Glycine max), 5'ss of exon 19
-GCTGCTAATGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTCATATTGTATGAAGAAGAAATTGCGgtaaacattcattgatcgatcaaaaagtggcatg--catcacccaattatttattttctcagatgaattttgtgcctggctattag-------
 ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||  |||| ||||||||||||||||||||||  ||| ||  |   |    |   |  |||   | | ||   | ||   | |  |    |  ||| | ||  |||  ||| |        
GGCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTTGTATTATATGAAGAAGAAATTGCggtaattattaataaaaacagttcactttaacattttcttaacatgactaagaaatggcctttactaatct-gtctctgtttataatggtttta

upper sequence: Vv18s0001g14680.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA14G40270.1 (Glycine max), 5'ss of exon 18
GCTGCTAATGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTCATATTGTATGAAGAAGAAATTGCGgtaaacattcattgatcgatcaaaaagtggcatg--catcacccaattatttattttctcagatgaattttgtgcctggctattag--------
||||||||||||||||| ||||||||||||||||||||||||||||||||||||||  |||| ||||||||||||||||||||||  ||| ||  |   |    |   |  |||   | | ||   | ||   | |  |     | |  | |||  |||  ||| |         
GCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTTGTATTATATGAAGAAGAAATTGCGgtaattattaataaaaacagttcactttaacattttcttaacatgactaagaaatggccgtactaa--tctgtctctgtttataatggttttag

upper sequence: Vv18s0001g14680.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: AT1G75850.1 (Arabidopsis thaliana), 5'ss of exon 18
GCTGCTAATGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTCATATTGTATGAAGAAGAAATTGCGgtaaacattcattgatcgatcaaaaagtggcatgcatcacccaattatttattttctcagatgaattttgtgcctg-gctattag-------------------------
|| || | |||||||||||||||||||||||||||||||||||| || || ||||| || || || || ||||||||||||||||   ||| |   ||  ||  |        | ||  |    || | | |   ||||| |  || ||| | | ||   ||||                           
GCCGCAAGTGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTTACCCAAGCATTTATGTTATACGAGGAAGAAATTGCGgtaat--ttcttcattctttctgagttaactttacacaaa--gataactaaaagtctcata-aaagtttatacttgcattattcttgtggtgcgttgtattataatatag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCTAATGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTCATATTGTATGAAGAAGAAATTGCGgtaaacattcattgatcgatcaaaaagtggcatgcatcacccaattatttattttctcagatgaattttgtgcctggctattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA