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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGCAACTGGAACAGGAATTGCCCCATTCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAGgtaagtttacactgaatggagtatagcttgaatcagaactattataattaagtcgtaatgtataaagctcataaattagtctacagtaaaatgaacttga...

Basic information

species Glycine max
transcript GLYMA11G08230.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08230.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 5
TTGGCAACTGGAACAGGAATTGCCCCATTCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAGgta---agtttacac--tgaat----ggagtata-gcttgaatcagaactattataattaagtcgtaatgtataaagctcataaattagtctacagtaa--aatgaacttga------------
 | || || || || || |||||||| ||||||||||| || ||||||||||| ||||||||| ||||||| |||||||||   |  || ||   | | |     || | || |||||  ||| ||   ||| |||| |  | | || | |  |  | ||   ||  | |    |||  |||     |||            
CTTGCGACCGGTACTGGTATTGCCCCGTTCCGCTCATTCTTGTGGAAAATGTTTTTTGAGAAGTATGATGACTACAAGgtaccaatgttgcatcattagttttcagactttatgcttgtttcaaaatc-ttaaaattcatactttatttctccaaatgatttttttctttgttttaaacaatatgtgtgaactcttgtgcag

upper sequence: GLYMA11G08230.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G168143_T01 (Zea mays), 5'ss of exon 5
TTGGCAACTGGAACAGGAATTGCCCCATTCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAGgtaagtttacactg-aatggagtatagcttgaat-cagaactattataattaagtcgtaatgtataaagctcataaattagtctacagtaaaatgaacttga
 | || || || ||||| || || || ||||| || ||  | ||||| |||||||||||||||||||| || |||||||||     |  | |   ||  ||| || |   |  | | ||    |     || |  |  |||     |||| |                            
CTTGCCACCGGTACAGGTATCGCTCCGTTCCGATCGTTCCTGTGGAAGATGTTCTTTGAGAAGCATGACGACTACAAGgtacaggcaggcagcggtgttgtaaagttcacacactggacagagaatggcaaataatg-tgtgagccgctcttgtgcag----------------------

upper sequence: GLYMA11G08230.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 5'ss of exon 6
TTGGCAACTGGAACAGGAATTGCCCCATTCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAGgtaagtttacactgaatggagtatagcttgaatcagaactattat-aattaagtcgtaatgtataaagctcataaatt-agtctac-agtaaaatgaacttga
 | | ||| ||||| ||||| || |||||| | |||||||| |||||||||||||||||| |||| || || |||||||| |      ||  || | |   |  ||  |  ||    | ||   |||||   |      ||     ||||  |||| | | | | | | | |||  |    
CTTGGAACAGGAACTGGAATAGCTCCATTCAGATCATTTTTGTGGAAAATGTTCTTTGAGGAGCACGAGGACTACAAGgtcaa-----accaaaagcaaact--ctctagacactgttgttgccaattataccactgactaacttactcaccaattgaatttgccaatcatatgtgcag--

upper sequence: GLYMA11G08230.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv04s0023g03510.t01 (Vitis vinifera), 5'ss of exon 6
TTGGCAACTGGAACAGGAATTGCCCCATTCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAGgtaagtttacactgaatggagtatagcttgaatcagaactattataattaagtcgtaatgtataaagctcataaattagtctacagtaaaatgaacttga----
 | ||||||||||| |||||||| || ||||||||||| || |||||||||||||||||||||||||| || ||||||||| |   ||  |||   |  |    | ||     | ||    | ||| |||    |||||  ||  || ||     |      |  | ||  | | | |    
CTTGCAACTGGAACTGGAATTGCTCCTTTCCGCTCATTCTTGTGGAAAATGTTCTTTGAGAAGCATGAAGACTACAAGgtagggcaactttgatatgtctgctacatgggcatgcaccggaa-aatgaag--aaaatgtccaat-ctaatcctgaacatggtaaaacaacaatcctaatgct

upper sequence: GLYMA11G08230.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv18s0001g14450.t01 (Vitis vinifera), 5'ss of exon 6
TTGGCAACTGGAACAGGAATTGCCCCATTCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAGgtaagtttacactgaatggagtatagcttgaatcagaactattataattaagtcgtaatgtataaagctcataaattagtctacagtaaaatgaacttga
 | |||||||| || || ||||| || || |||||||| || |||||||||||||| |||||  |||| || |||||||||  |      | ||| || |||   |  || ||      |   |||   ||  | ||||   |  ||  |   | |   |    |  |          
CTTGCAACTGGTACTGGCATTGCTCCTTTTCGCTCATTCTTGTGGAAAATGTTCTTCGAGAAATATGAAGACTACAAGgtagatgagatatcaatagattatgtatcaaagcactgaattgtgaatcttgtgatcatgttagagacttgt--ttcaacttgtcatgcag---------

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|120534406|gb|EH262539.1|EH262539
EST:     TCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAG                         TTTCA-TGGTTTGGCATGGCTC
genomic: TCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAGgtaagtttac ... atttatgtagTT-CAATGGTTTGGCATGGCTC
EST: gi|9983988|gb|BE658096.1|BE658096
EST:     TCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAG                         TTCAATGGTTTGGCATGGCTCTTCTTGGGTGTCCCCACAAGCAGCTCACTA
genomic: TCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAGgtaagtttac ... atttatgtagTTCAATGGTTTGGCATGGCTCTTCTTGGGTGTCCCCACAAGCAGCTCACTA
EST: gi|21637544|gb|BM107699.1|BM107699
EST:     GAGAAGCATGATGATTACAAG                         TTCAATGGTTTGGCATGG-TCTTCTTGGGTGTCCCCACAAGCAGCTCATTA
genomic: GAGAAGCATGATGATTACAAGgtaagtttac ... atttatgtagTTCAATGGTTTGGCATGGCTCTTCTTGGGTGTCCCCACAAGCAGCTCACTA
EST: gi|120534689|gb|EH262822.1|EH262822
EST:     TCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAG                         TTCAATGGTTTGGCATGGCTCTTCTTGGGTGTCCCCACAAGCAGCTCACTA
genomic: TCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAGgtaagtttac ... atttatgtagTTCAATGGTTTGGCATGGCTCTTCTTGGGTGTCCCCACAAGCAGCTCACTA
EST: gi|16342619|gb|BI968214.1|BI968214
EST:     TCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAG                         TTCAATGGTTTGGCATGGCTCTTCTTGGGTGTCCCCACAAGCAGCTCACTA
genomic: TCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAGgtaagtttac ... atttatgtagTTCAATGGTTTGGCATGGCTCTTCTTGGGTGTCCCCACAAGCAGCTCACTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGCAACTGGAACAGGAATTGCCCCATTCCGCTCATTTTTATGGAAAATGTTCTTTGAGAAGCATGATGATTACAAGgtaagtttacactgaatggagtatagcttgaatcagaactattataattaagtcgtaatgtataaagctcataaattagtctacagtaaaatgaacttga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC