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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaagcttttgttctttagttaagaactttgtattatctgattcttctggtggtgataaaattgatcaatatttttttgtctctgcag

Basic information

species Glycine max
transcript GLYMA08G01040.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os05g01240.2 (Oryza sativa), 5'ss of exon 14
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGg------taaatcaagcttttgttcttta-gttaagaactttgtattatctgattcttctgg-tggtgata-------aaattgatcaatat---ttttttgtctctgcag-----------------------------------
| || | ||||||||||| ||||| || ||||||||||||||||||||| | || || ||||| || ||||| | |||||| |||||||| || |||| ||      ||  || ||   || || | ||   |||  |     ||| |       ||||||  ||    ||       ||| ||||  | ||     |||| |   |                                       
TGCTTTGATTGCTCATTTTCAGAATTCTAGCCTGATGAATGAAGACAAATGGTGTCGACCTATGCTTTTCCACAAAGATGGTCCAAATGCAGGAGATCAGgtgtgaatatctctagtgcttattgtatacactaaatataccatatgagtgaccacttctgactgaccctattcgcacaaaatgattgacatggcggttttatacatattattattttctgataaagatacatattattattgcag

upper sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 5'ss of exon 14
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgta-aatcaagcttttgttctttagttaagaactttgtattatctgattcttctggtggtgataaaattgatcaatatttttttgtc----tctgcag--
  ||||||||||||| ||||||||||| ||  |||||||||| ||||| || ||||| || || || |||||| | ||||| || ||||| || |||| ||||  |||   || |   ||| |   |       |     | |||     |  |    |   | |||       ||     || | |    | ||| |  
AGCTCTTATTGCTCACTTCCAGAACTCCAGTTTGATGAATGAGGACAAGCGCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAGgtatgatctttctctctctctctctctctctctctctctctctctctcgttgataaatggagttaaagcagcagatgacacttggacacagtttgctgtt

upper sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G459746_T01 (Zea mays), 5'ss of exon 14
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaagct----tttgttctttagttaagaactttg-tattatctgattcttctggtggtgataaaattgatca----atatttttttgtctctgcag
  |||| |||||||||||||||||||| ||  |||||||||| |||||||||||||| || || ||||||||  ||||||| || ||||| || |||| ||||     |  |    ||| || | | |||   |  ||   |  |||||  |||| |  ||     ||   ||           | | |   |  ||| |  
AGCTCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGTTGCCGCCCCATACTCTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttatttcttttttattttgtcgttggtactttccctgctatcttgttctcc-agttacattatgtttcgctgcagtgcactgtgacgagtcttct-

upper sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G156956_T01 (Zea mays), 5'ss of exon 13
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaagcttttgttctttagttaa-gaactttgtattatctgattcttctggtggtgataaaattgatcaatatttttttgtctctgcag
  || | ||||||||||||||||| || ||||||||||||||||| ||| | ||||| ||||| || ||||| | ||||||||| || || || || | ||||   |  |   || |  | | ||    |  |  ||||    |   ||  |    ||    | |    ||     ||   ||  | || |   
CGCTTTGATTGCTCATTTCCAGAATTCTAGCCTGATGAATGAAGAGAAATGGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgta---cgggtaattatcttgttgtcggcgctcgctgtacctccatgtttgtgcaatgac--tgacgcagagttgcatccgttcttatcag---

upper sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G451716_T01 (Zea mays), 5'ss of exon 14
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaagcttttgttctttagttaagaactttgtattatctgattcttc-tggtg-gtgataaaat--tgatcaatatttttttgtctctgcag-----------
  ||||  ||||||||||||||||||||||  |||||||||| || ||||| ||||| ||||| ||||||||  | ||||| || ||||| || ||||  |||          |||| | | |        || | ||||||||| | | || ||||   |||  | ||  |||  | || ||  |   |||||| |           
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctctacttgtccatca--------ctctctattatctgttgcatcatggtatatgactatatggtgactagtagttcctgaactctgctgcttatcgcata

upper sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 4
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaagcttttgttctttagttaagaactttgtattatctgattcttctggtggtgataaaattgatcaatatttttttgtctctg-cag---------
  | || |||||||||||||||||||| ||  |||||||||| |||||||| ||||| || || || |||||  ||||||| || ||||| || |||| ||||     |  || | || | |   |  | |||||   |   |||  | ||     ||| | |  ||  |    | | || |    | || ||          
AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttattttgtattttgtc-ctgggtactttccctc--ctgtctttttctccggttacattatgtactgttgtcttgtgagttgtgacaagtcttctct

upper sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 5'ss of exon 13
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaagcttttgttctttagttaagaactttg----tattatctgattcttctggtggtgataaaattgatcaatatttttttgtct-ctgcag--
  |||||||||| |||||||||||||||||  ||||||| ||||||||||||||| | |||||||||||||| || | ||| |||||||||||||||| |||||   |  |    | ||  | | ||      ||     ||| | ||  ||||  ||   || || | ||       || || | | |   ||  ||  
AGCTCTTATTGCCCATTTCCAGAACTCAAGTTTGATGAACGAAGACAAACGTTGCAGGCCTATTCTCTTCCACACTGCTGGTCCAAATGCTGGTGATCAGgtaaggaagacaagggctcaattgatatccttattcaaactataacctctttctgttgcaagtaatcatatcatctggtagttatgtattcactatagcg

upper sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaa--tcaagcttttgttc-------tttagttaagaactttgtat---tatctgattcttctggtggtgataaaattgatcaatatttttttgtctctgcag----------------------------------------------
  |||||||||| |||||||||||||||||| | ||||| ||||||||||||||||| |||||||||||||| || ||||| |||||||||||||||| ||||||  | ||   ||  | |       | | |||  |  |    |||   |||    ||| |    |     |   |||  ||| ||| |  |    |  |                                                 
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatt--tcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag

upper sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaagcttttgttctttagttaagaactttgtattatctgattcttctggtggtgataaaattgatcaatatttttttgtctctgcag------------
| ||||||||||||||||||| ||||| ||| |||||||||| || ||||||||||| |||||||| || ||||| ||||| |||||||| ||||||| ||||   ||    | ||  | | |  || |  || | | || |       |   ||  || |     || |  |||||| |||  |||     |            
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggaca----tctga-cataaagtatgttctctattttgttgttggatctcggatgtaaacctgtttaagaatattctttattctaattggtaatgactatta

upper sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
lower sequence: EFJ29693 (Selaginella moellendorffii), 5'ss of exon 11
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaagcttttgttctttagttaagaactttgtattatctgattcttctggtggtgataaaattgatcaatatttttttgtctctgcag
| | ||  | || |||||||| ||||||||||| ||||| ||||||||  | |||||||| ||||| || | | | || || || ||    || ||||| ||||   |  ||           |   |||  ||||||   ||| | | |  |  | |          |                        
TGCCCTCGTCGCACATTTCCAAAACTCAAGCCTCATGAACGAAGACAAGAGATGCCGTCCAATTCTGTTTCGTTCGGAAGGTCCCAACCTGGGCGATCCTgtaagcaatact-----------gcggagacttttgtacattctaactttcttttttggatcttggcag------------------------

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|22539931|gb|BU089774.1|BU089774
EST:     GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCG                         GAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
genomic: GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaag ... gtctctgcagGAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
EST: gi|8670017|gb|BE191124.1|BE191124
EST:     GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCG                         GAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
genomic: GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaag ... gtctctgcagGAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
EST: gi|22932879|gb|BU550018.1|BU550018
EST:     TCCATACAGATGGCCCAAATGCTGGTGATCCG                         GAGCCTTTCCCCATGNNTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
genomic: TCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaag ... gtctctgcagGAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
EST: gi|9258493|gb|BE346640.1|BE346640
EST:     GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCG                         GAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
genomic: GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaag ... gtctctgcagGAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
EST: gi|9259799|gb|BE347946.1|BE347946
EST:     GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCG                         GAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
genomic: GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaag ... gtctctgcagGAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
EST: gi|13480999|gb|BG510342.1|BG510342
EST:     GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCG                         GAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
genomic: GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaag ... gtctctgcagGAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
EST: gi|8670012|gb|BE191119.1|BE191119
EST:     GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCG                         GAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
genomic: GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaag ... gtctctgcagGAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
EST: gi|58014871|gb|CX701613.1|CX701613
EST:     GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCG                         GAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC
genomic: GTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaag ... gtctctgcagGAGCCTTTCCCCATGGGTGCCAATATTAGACTGAGACCCGGAAAATCTCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaagcttttgttctttagttaagaactttgtattatctgattcttctggtggtgataaaattgatcaatatttttttgtctctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG