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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaacttgtgtaatattgtatgacatttgtatctctaaatgtagttgtttgatggcttgtattttaacaggcctatttatttataagacaagctgct...

Basic information

species Glycine max
transcript GLYMA06G15380.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15380.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os04g34940.1 (Oryza sativa), 5'ss of exon 4
TTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaag--aacttgtgtaatat-tgtatgacatttgtatctctaaatgtagttgtttgatggc-ttgtattttaacaggcctatttatttataagacaagctgct
  | |||||||| |||||||||||  |||| || ||||| ||||||||||| ||  |||||||||||||  | |||||||   | || || | | | |   |  | |||  || | |      |    | | |  |   | || ||  | | |  ||||  |   ||   |||| |   
CCTTGAGACTACCCGCCATGTTTCCTTGATTACCATTACATTGTCAAAGAAGGAGCTGGATACGTCATCTCCTGGgtaagtagaattctgcactttcttcctcccctttcgattttttgtaaaaaaaatctaagagagctctagttggatatgattatt-gtcagtagttcaagat---

upper sequence: GLYMA06G15380.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv07s0031g02040.t01 (Vitis vinifera), 5'ss of exon 6
TTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaacttgtgtaatattgtatgacatttgtatctctaaatgtagttgtttgatggcttgtattttaacaggcctatttatttataagacaagctgct----------
  | |||||||| || || |||||||||||||||||||| ||||||||||| ||  ||||||| || ||| | ||||||       || | |||   ||   ||||  || |  |||| ||   |   ||  |||| |||||    |    | ||  |||||| |    |  | |          
CCTAGAGACTACCCGTCACGTTTCAATGATCACAATTACTTTGTCAAAGAAGGAGCTGGATACATCCTCCACAGGgtaaa------tgaactatg--attgtatttccatgttaaaatttaagagg--gaatgcttttatttatttatttattttattttatatggtgtgtagttgtgtagcttt
















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|298190263|gb|HO032384.1|HO032384
EST:     ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGG                         ATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCT
genomic: ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaactt ... tctcatgcagATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCT
EST: gi|254343935|gb|GR857691.1|GR857691
EST:     ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGG                         ATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
genomic: ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaactt ... tctcatgcagATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
EST: gi|120534511|gb|EH262644.1|EH262644
EST:     ATGATCACAATTACCTTGTCAAAGAAAGAATNGGATACGTCATCCGCGGG                         ATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAA-ATGA
genomic: ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaactt ... tctcatgcagATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
EST: gi|298186819|gb|HO037452.1|HO037452
EST:     ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGG                         ATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
genomic: ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaactt ... tctcatgcagATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
EST: gi|120534428|gb|EH262561.1|EH262561
EST:     ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGG                         ATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAA-ATGA
genomic: ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaactt ... tctcatgcagATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
EST: gi|120530869|gb|EH259002.1|EH259002
EST:     ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGG                         ATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAA-ATGA
genomic: ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaactt ... tctcatgcagATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
EST: gi|298175747|gb|HO018344.1|HO018344
EST:     ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGG                         ATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
genomic: ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaactt ... tctcatgcagATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
EST: gi|15337539|gb|BI498195.1|BI498195
EST:     ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGG                         ATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
genomic: ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaactt ... tctcatgcagATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
EST: gi|20449683|gb|BQ253807.1|BQ253807
EST:     ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGG                         ATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
genomic: ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaactt ... tctcatgcagATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
EST: gi|24136070|gb|BU926580.1|BU926580
EST:     AATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGG                         ATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
genomic: AATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaactt ... tctcatgcagATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
EST: gi|298172713|gb|HO019753.1|HO019753
EST:     ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGG                         ATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
genomic: ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaactt ... tctcatgcagATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
EST: gi|254343936|gb|GR857692.1|GR857692
EST:     GATCACAATTACC-TGTCAAAGAAAAGAATGGGATACGTCATCCCGCGGG                         ATACCAACATCCTCTTCCAGTTGATCAAGTAAAACC-TTAAATGAATATG
genomic: GATCACAATTACCTTGTCAAAG-AAAGAATTGGATACGTCAT-CCGCGGGgtaagaactt ... tctcatgcagATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATG
EST: gi|26268500|gb|CA819563.1|CA819563
EST:     ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGG                         ATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA
genomic: ATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaactt ... tctcatgcagATACCAACATCCTCTTCCAGTTGATCAAGTAAAACCTTTAAATGAATATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGAGACTACTCGCCATGTTTCAATGATCACAATTACCTTGTCAAAGAAAGAATTGGATACGTCATCCGCGGGgtaagaacttgtgtaatattgtatgacatttgtatctctaaatgtagttgtttgatggcttgtattttaacaggcctatttatttataagacaagctgct

- - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA