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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctattttcttattcccttccttgaaatatcaaactcttctattcatatctcaaaaccttgccaggtcccactgtgcaatttgacctctgctacaaatt...

Basic information

species Glycine max
transcript GLYMA02G39360.1
intron # 27
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 27
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 27
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctattttcttattcccttccttgaaatatcaaactcttctattcatatctcaaaaccttgccag--gtcccactgtgcaatttgacctctgctacaaatt--
||| || ||||||||  | |||||||| || ||||| || ||||| || ||||||||||| || || ||||| ||||||||||| || || ||||| ||||| |  |||   |  || |   ||    ||||  | | || | || |    | |  |  | |   |  |    |   || ||  |  ||    || | | ||  
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgtttgattta--agcccataaatttc--tatcttatttttgtgttgaatatttagcatgtagtatgctgcattaacttgtaacattgccatctcttctagttat

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 27
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctattttcttattcccttccttgaaatatcaaactcttctattcatatctcaaaaccttgccag--gtcccactgtgcaatttgacctctgctacaaatt--
||| || ||||||||  | |||||||| || ||||| || ||||| || ||||||||||| || || ||||| ||||||||||| || || ||||| |||||  | |||   |  || |   ||   || |     | || | || |    | |  |  | |   |  |    |   || ||  |  ||    || | | ||  
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaattta--agcccataaatttctattttg--tttttgtgttgaatatttagcatgtagtatgctgcattaacttgtaacattgccatctcttctagttat

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctatttt---cttattcccttccttga-aatatcaaact--cttctattcatatctcaaaaccttgccaggtcccactgtgcaatttgacctctgctacaaatt--------------------
 ||||| ||||| ||  | |||||||| |||||||| || ||||| |||||||||||||||||||| |||||||| |||||||| || ||||| |||||||| |  ||    |  ||||  ||   ||| ||||| | |||  |    |   |  ||  ||   | |     |||  |||  ||| |     ||      |||||                     
ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattctattgactgataatatgagactagcgataagctaattcataaggtcctagtctgtct-acttggcattgcattctgattagcaaatccatccattcatgtaacacag

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 4
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctatttt---cttattcccttccttgaaat-atcaaactctt--ctattcatatctcaaaaccttgccaggtcccactgtg-caatttgacctctgctacaaatt----------------------------
 ||||| ||||| ||  | |||||||| |||||||| || ||||| |||||||||||||||||||| |||||||| |||||||| || || || |||||||| |  ||    |  ||||||||   ||| || |  | |||  |    |   |  ||   | ||   |  |||||| | | || | | ||| | |    | |  |||                            
ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAGgtttggttcaaacccattcccttgactgatattacgagactagtgataagctaattcagtatacgccgtaaggtcctagtctgtctacttggcatagcattctgattagcaaacacatccaatcatgtaacacag

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 12
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctatttt---cttattcccttccttga-aatatcaaactcttctattcatatctcaaaaccttgccaggtcccactgtgcaatttgacctctgctacaaatt------------------
 || || ||||||||  | ||||||||||| ||||| || ||||| |||||||| ||||||||||| |||||||| ||||| || || || ||||||||||| |  ||    |  |||   ||   |||  ||||   | |     |||||   ||  | ||      |||        |||| | |||    |   ||  ||                   
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTATCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaggcgtatgcttgcattctgattagtaa-acgcatccaatcatatgtaatgcag

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctatttt---cttattcccttccttga-aatatcaaactcttctattcatatctcaaaaccttgccaggtcccactgtgcaatttgacctctgctacaaatt------------------
 || || ||||||||  | ||||||||||| ||||| || ||||| |||||||| ||||||||||| |||||||| ||||| || || || ||||||||||| |  ||    |  |||   ||   |||  ||||   | |     |||||   ||  | ||      | |        |||| | |||    |   ||| ||                   
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgcttgcattctgattagtaa-acacatccaatcatatgtaatgtag

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 7
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctatttt---cttattcccttccttga-aatatcaaactcttctattcatatctcaaaaccttgccaggtcccactgtgcaatttgacctctgctacaaatt------------------
 || || ||||||||  | ||||||||||| ||||| || ||||| |||||||| ||||||||||| |||||||| ||||| || || || ||| ||||||| |  ||    |  |||   ||   |||  ||||   | |     |||||   ||  | ||      |||        |||| | |||    |   ||| ||                   
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTAAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaggcgtatgcttgcattctgattagtaa-acacatccaatcatatgtaatgcag

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 12
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctattttcttattcccttccttgaaatatcaaactcttc--tattcatatctcaaaaccttgccaggtcccactgtgcaatttgacctc-tgctacaaatt
 || || ||||||||  | ||||||||||| ||||| || ||||| |||||||| ||||||||||| |||||||| || || || || || ||||||||||| |  || |  |  |  |   |||    || | |    ||    ||   |   | |    |  |  || |     ||| ||| |  |  | |||  ||    
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTTCTCGTGTATTTCATTGAGCAGgtttggtt-cgaacccattgtattggctgatgatatgtgtcggcgtttcgagaccgaggggtccctgggccgacgagtgaaatgtcgctgcgtgccccagc--

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM2G115138_T01 (Zea mays), 5'ss of exon 11
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctatttt---cttattcccttccttga-aatatcaaactcttctattcatatctcaaaaccttgccaggtcccactgtgcaatttgacctctgctacaaatt------------------
 || || ||||||||  | ||||||||||| ||||| || ||||| |||||||| ||||||||||| |||||||| ||||| || || || |||||| |||| |  ||    |  |||   ||   |||  ||||   | |     |||||   ||  | ||      |||        |||| | |||    |   ||  ||                   
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGAAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaggcgtatgcttgcattctgattagtaa-acgcatccaatcatatgtaatgcag

upper sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 27
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 27
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctattttct-tattcccttccttgaaatatcaaactcttctattcatatctcaaaaccttgccaggtcccactgtgcaatttgacctctgctacaaatt-
|||||| |||||||| || ||||| ||    ||||| || |||||||| ||||| || ||||||||  ||||||| ||||||||||| || ||||||||||| |   |  | ||  |   ||  | |||  | ||| |    || ||||   |||||  ||    || |   | ||| |  |   |  | | |||    || 
GTCAAAGAAAGACAACCTATACAAAGATGCGATGGAGACATGCTCTCAGTCTGGGGATCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAGgtatgagtcatatacacttgtctataaaagctgaaattgagataatcat-catcaaatgctaaatag-tgtgaatgttccttcataaattttctaattttta

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|58016487|gb|CX703229.1|CX703229
EST:     CTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAG                         GGGAAGAAGGAATGTTTTGCATCTTGCCTCTTCGTCTGTTATGATATAATA
genomic: CTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctattttc ... atctttccagGGGAAGAAGGAATGTTTTGCATCTTGCCTCTTCGTCTGTTATGATATAATA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctattttcttattcccttccttgaaatatcaaactcttctattcatatctcaaaaccttgccaggtcccactgtgcaatttgacctctgctacaaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttcc