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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACGATGCTTCACAACGCCCATCCTCCTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtgtctcgagaatggttatgttcatagttcaaattgcagcctccatttggaaactaacggtttttgtataccttgtatatatgcag

Basic information

species Vitis vinifera
transcript Vv02s0025g02980.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 5'ss of exon 2
TACGATGCTTCACAA-CGCCCATCCTCCTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtg----tctcgagaatggttatgttcatagttcaaattgcagcctccatttggaaactaacggtttttgtataccttgtatatatgcag
  |   ||  | ||  ||| |  |     | || ||||||||||| || ||  |||| |||||||| || ||||| ||||| ||||||||||||||||| ||| ||    | ||         | | || || | |||     || |  | || ||| |   | |   | |    ||  |||  |  |     
-GCTGGGCAGCCCAGGCGCGCCCCTAAGCTCAACGAGAGGATCCTGTCCTCCTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaactgtctttcccatctctctttatggctcac-ccacaaca-ctatgtggcatgcatca--tctcacttaatttggttcaacag--

upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os10g26600.1 (Oryza sativa), 5'ss of exon 2
TACGA-TGCTTCACAACGCCCATCCTCCTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtgtct-cgagaatggttatgttcatagttcaaattgcagcctccatttgga---aactaacggtttt-tgtataccttgtatatatgcag-----
 | |  ||    | |     |  | | | |||||||| ||||||| || ||  | || | | |||| || ||||| ||| |||||||||||||||||||||||  ||    |  ||  | || |||     | || | ||    |||| ||| |    | || | | |  |   | | || | |  | |||| |     
-ATGGCTGAAGAAAAGAAGACCCCATGCCTGAATGAGCGGATCCTGTCGTCGCTCTCGAAGCGATCCGTGGCTGCGCATTCCTGGCATGATCTTGAGATTGgtaagtagatgtcaagagataagtt----atccatagtgttctctccttttcggtgtagctgatgctgatgcattttccctctccaaatgctgtatag

upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G061928_T04 (Zea mays), 5'ss of exon 2
--TACGATGCTTCACAACGCCCATCCTCCTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtgtctcgagaatggttatgttcatagttcaaattgcagcctccatttggaaactaacggtttttgtataccttgtatatatgcag
  |  |  ||   | |  |||| |   |    ||||| ||||||||||| ||  |||| ||||| || || ||||||||||| ||||||||||||||||| |||  ||    | ||   |  | |   | | ||   ||  | |  |  ||||  || |||   |      ||   || |   ||| |||
GCTGAGCAGCCGAAGAGGGCCCCTAAGCTC--AATGAAAGGATCCTCTCTTCTCTGTCCAGGAGGTCCGTAGCTGCTCATCCATGGCATGATCTTGAGATCGgtacgttggcacaactatcctttc--ttgctc---ttctaactcc--tttgtcaaataagcatacactaattgattttggttatacag

upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G104918_T03 (Zea mays), 5'ss of exon 2
--TACGATGCTTCACAACGCCCATCCTCCTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtgtctcgagaatggttatgttcatagttcaaattgcagcctccatttggaaactaa---cggtttttgtatacc-ttgtatatatgcag
  |  |  || | | |  |||| |   |    ||||| ||||||||||| ||  |||| ||||| || || ||||||||||| ||||||||||| ||||| |||| ||  |   | |     |  |     | | || | |    |   | ||  || |||      |   | || | | || |   |||||||
GCTGAGCAGCCTAAGAGGGCCCCTAAGCTC--AATGAAAGGATCCTCTCCTCTCTGTCCAGGAGGTCCGTAGCTGCTCATCCATGGCATGATCTCGAGATCGgtgcgtgactcaactatcctttcttgctctcctaactcctatgtggctctgtcaaataagcatactccatctaaatcattttggttatgcag

upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA19G45050.1 (Glycine max), 5'ss of exon 1
TACGATGCTTCACAACGCCCA---TCCTCCTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtgtctcgagaatggttatgttcatagttcaaattgcagcctccatttggaaacta-acggtttttgtataccttgtatatatgcag
   | ||    | | || |||    ||   |||||||| ||||| || |||||| ||||||||||||| || ||||||||||| ||||||||||| || ||||||   | |      || |  | ||  | ||||| || | |   |  |  |  |||  | |         ||     | |  ||||||||
---GCTGGAGAAAATCGTCCAGTTCCCCGTTTGAATGAAAGGATTCTTTCATCATTGTCAAGGAGATCAGTAGCTGCTCATCCTTGGCATGATCTAGAAATTGgtaacttt----gctgatattattgcttgttcatatagtatagttaagatttaaatcatattacaaaactacttaattttcatatgcag

upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA16G01960.1 (Glycine max), 5'ss of exon 1
-TACGATGCTTCACAACGCCCATCCTCCTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtgtctcgagaatggttatgttcatagttcaaattgcagcctccatttggaaactaa-----cggtttttgtat-accttgtatatatgcag-----------------------------------------------------------------------------------
   |||     |    ||     |   ||||||||| ||||| || |||||  |||| |||||||| ||||||||||| || |||||||||||||| ||||||   ||| |    ||  || |||  |   |   |||  |     ||||     ||| |       |||  | ||| | |||||   || ||                                                                                     
CCTCGAGAAAACCGTCCGGTT-CCACGCTTGAATGAAAGGATTCTTTCATCTCTGTCTAGGAGATCAGTTGCTGCTCACCCTTGGCATGATCTTGAAATTGgta-atcttgttgttgactacgttgcttcattgcatttaatttaacattgaatgacttaaaatcaagttgctatattatcttgtggctaggccaaatgcttatgctaaatcaaggattattttggtcttagcctacaaaaaaaaaaagttgttaatgttcttaggtttcatatgcag

upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA18G18510.1 (Glycine max), 5'ss of exon 1
TACGATGCTTCACAACGCCCA---TCCTCCTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtgtctcgagaatggttatgttcatagttcaaattgcagcctccatttggaaactaacggtttttgtatacct--tgtatatatgcag
    |||    | | || |||     ||  |||||||| ||||| || |||||| ||||||||||||| || ||||| ||||| ||||||||||| || ||||||   | |      || |  | ||  | |||||  | | |   |  |  |  |||  |    ||      ||| |  | |  ||||||||
----ATGGAGAAAACCGTCCAGTTCTCTATTTGAATGAAAGGATTCTTTCATCATTGTCAAGGAGATCAGTAGCTGCCCATCCTTGGCATGATCTAGAAATTGgtaacttt----gttgatattattgcttgttcatgtagtatagttaagatttaaatca-tatttcaaaactacttaattttcatatgcag

upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA07G05390.1 (Glycine max), 5'ss of exon 2
TACGATGCTTCACAACGCCCATCCTCC--TTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtgtctcgagaatggttatg-ttcat-agttcaaattgcagcctccatttggaaactaacggtttttgtata---ccttgtatatatgcag---------------------------------------------------------------------------------
  |  |||   |     ||  | | ||  || ||||| ||||| || |||||  |||| |||||||| ||||||||||| || |||||||||||||| ||||||   ||| |   |   || || |||||  |     | |  | | || | |  ||    ||   | ||  ||||   ||||||   || ||                                                                                   
--CCTTGCGAAAACCGTCCGGTTCCCCGTTTAAATGAAAGGATTCTTTCATCTTTGTCTAGGAGATCAGTTGCTGCTCACCCTTGGCATGATCTTGAAATTGgtac-tcttgttcacttttttgcttcattggcatttactttaacatcgaat--gacttaaatcatgttgctatatccccttgtggctaggccaaatatgcttatgccaaaacaaggactagtttggtcttaccccacaaaaaaagttgttaatgttcttaggtttcatgtgcag

upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA11G18100.1 (Glycine max), 5'ss of exon 1
TACGATGCTTCACAACGCCCA--TCCTC-CTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtgtctcgagaatggttatgttcatagttcaaattgcagcctccatttggaaactaacggtttttgtatacct--tgtatatatgcag
   | ||    | |  | |||  |||||  |||||||| ||||| || |||||| | ||||||||||| || | ||| ||||| ||||||||||| || ||||||   | |      || |  | ||  | ||||| || | |   |  |  |  |||  |    ||      ||| |  | |  ||||||||
---GCTGGAGAAAATTGTCCAGTTCCTCATTTGAATGAAAGGATTCTTTCATCATTATCAAGGAGATCAGTAGTTGCCCATCCTTGGCATGATCTAGAAATTGgtaacttt----gttgatattattgcttgttcatatagtatagttaagatttaaatca-tatttcaaaactacttaattttcatatgcag

upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 2
TACGATGCTTCA-CAACGCCCATCCTCCTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtgt------ctcgagaatggttatgttcatagttcaaattgcagcctccatttggaaactaacggtttttgtataccttgtatatatgcag
   || ||| || | ||   |  |     | || |||||||| ||||||||  ||||||| ||||| || ||||||||||| ||||||||||||||||||||| | |       || | |   | ||  ||   | |||| | |   |  | |  ||   || | |    | | | |||   | | ||       
-CAGAGGCTGCAGCGACCAGCTCCTCGTCTTAACGAGAGGATTCTCTCATCCTTGTCAAGAAGATCCGTAGCTGCTCATCCATGGCATGATCTTGAGATTGgtatataaatcattctaaacatgctactttttgatttcatacttttgtattctgttactaaatcataagtctgg-ataatctatctag------

upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT4G01480.1 (Arabidopsis thaliana), 5'ss of exon 2
TACGATGCTTCACAACGCCCATCCTC-CTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtgtctcgagaatggttatgttcatagttcaaattgcagcctccatttggaaactaacggtttttgtatacc-ttgtatatatgcag
 | || |||||| ||| |   ||| |  || || |||||||| ||||||||  |||| | ||||||||||||||| ||||| |||||||||||||| || |||        | |||   | | || |   |   | |    |  |    || ||  ||     |||   || |   || ||| | |||||
-AAGAAGCTTCAGAACCCTACTCCACGTTTAAACGAGAGGATTCTCTCATCTTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgta-------ataatcactgttttaaagat---attctgtgtgtttgattagagtctt----tttaactaaattgttctatgtgtgcag

upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 5'ss of exon 2
TACGATGCTTCACAACGCCCATCCTCCTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgt-------------gtctcgagaatggttatgt-tcatagttcaaattgcagcct--ccatttggaaactaacggtttttgtataccttgtatatatgcag-------------
                             ||| |||||||| |||||| || | || |||||||| || ||||| ||||| ||||| || ||||||||||||               ||||  |   ||||  ||| || ||  | | |   ||      || | |  || ||  |  | | | |    ||  ||   |   ||             
-----------------------------GAACGAGAGGATTCTCTCAACACTATCCAGGAGATCTGTAGCTGCACATCCATGGCACGACCTTGAGATTGGTCCTGAAGCTCCATTGGTCTTCAATGTGgtattgtctcttaacttataacccaagtaagccttctttaatctctctctctctcttggtctgttaacgagagagcctctctggtcag

upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 3
TACGATGCTTCACAACGCCCATCCTCCTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtg-----tctcgagaatgg--ttatgttcatagttcaa-attgcagcctccatttggaaactaacggtttttgtataccttgtatatatgcag----
 |   |||    || |  ||| |  |  | ||  |  | ||  | ||| |||||    |  ||||||||||||| ||||| |||||||||||||| |||||||||      || |  ||| |   ||| |   || |||   |||      |  ||||    | |     |||||||   | |||| |  ||        
AATTCTGCGGTTCATCAACCAGCACCACTCAACCACCGCATTTTGTCAACAATGGATCGACGATCGGTTGCTGCACATCCGTGGCATGATCTTGAAATTGgtgtggatctccttgtcaatagatctatttctttatttctttatttttatttttatttctttatttttattttttgtgatctttgtgttcataagaagtt

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACGATGCTTCACAACGCCCATCCTCCTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtgtctcgagaatggttatgttcatagttcaaattgcagcctccatttggaaactaacggtttttgtataccttgtatatatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT