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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGACCAACAGAAGAATAATGCCACCAAGAAAGACAAACCTGCTGCTGAGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgcttttgttggttttctaaagacatatctacctttatttttataacatacttttggttctataatgtctttgcaatatcatttgtaatttgtat...

Basic information

species Zea mays
transcript GRMZM5G823855_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G823855_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g01250.1 (Oryza sativa), 5'ss of exon 11
TTTGGACCAACAGAAGAATAATGCCACCAAGAAAGACAAACCTGCTGCTGAGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgcttt---tgttggttttctaaagacatatctacctttatttttataacat-acttttggttctataatgtctttgcaatatcatttgtaatttgtat
|||||||| |||||| || || ||||||||||| ||||||||||||||| | || ||||| || ||||||||  ||||||||||||||||||||||||| || |||  | |   |||      | || | || | ||| |  || ||||||| | || |    | |||| ||| ||     |     |      |||  ||   
TTTGGACCTACAGAAAAACAACGCCACCAAGAAGGACAAACCTGCTGCTAAACCAATAATAGTCCCAATTGTGTTGAGGATGTCTGATTTTGATCACAAGgtctgttttctctgtgtcacaaatttagatacttgtctgctcttttttttattaaattaaacctagttccatattgggaaagaggagtt-cgcataagatg---

upper sequence: GRMZM5G823855_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g28260.1 (Oryza sativa), 5'ss of exon 14
TTTGGACCAACAGAAGAATAATGCCACCAAGAAAGACAAACCTGCTGCTGAGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgct---tttgttggttttctaaagacatatctac-ctttatttttat-aacatacttttggttctataatgtctttgcaatatcatttgtaatttgtat
|||||||| |||||| || ||  |||||||||| ||||||||||||||||| || ||| | || ||||||||  ||||||||||||||||||||||||| || |||  |   | |||      | || | || | | | | |||| ||||||| ||  ||    | |||| ||| ||     |     |  |   |||  |    
TTTGGACCTACAGAAAAACAACACCACCAAGAAGGACAAACCTGCTGCTGAACCAATAGTAGTCCCAATTGTGTTGAGGATGTCTGATTTTGATCACAAGgtctgttttctctctgtcacaaatttagatacttttatgctctttgtttttattaaattaaacctagttccatattgggaaagaggagtt-tgcataagat----
















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|32845909|gb|CD985590.1|CD985590
EST:     TACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: TACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|5901422|gb|AW042522.1|AW042522
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|148949248|gb|EC894691.2|EC894691
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|24766527|gb|CA401677.1|CA401677
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|88755879|gb|DY540020.1|DY540020
EST:     GTACTGAGGAGGTCTGATTTTGATCCCAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: GTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|60339553|gb|DN206526.1|DN206526
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|71321743|gb|DR797565.1|DR797565
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|211298031|gb|FL348697.1|FL348697
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|211480575|gb|FL334477.1|FL334477
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|113702722|gb|EE680226.1|EE680226
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|60351335|gb|DN218308.1|DN218308
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|5566891|gb|AI881802.1|AI881802
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|211460116|gb|FL447906.1|FL447906
EST:     GATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: GATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|5922116|gb|AW055510.1|AW055510
EST:     TCCAATTGTACTGAGGATGTCTGATTTTGATCNCAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: TCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|6742560|gb|AW313375.1|AW313375
EST:     CGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCGCAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: CGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|149108522|gb|EE189694.2|EE189694
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|5650324|gb|AI920684.1|AI920684
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCNCAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|24764891|gb|CA400053.1|CA400053
EST:     CGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: CGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|5871658|gb|AW018129.1|AW018129
EST:     CAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: CAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|60350932|gb|DN217905.1|DN217905
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|5804752|gb|AI979722.1|AI979722
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|5819327|gb|AI987533.1|AI987533
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|60348857|gb|DN215830.1|DN215830
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAGCCACTAGAGCTTTCAGAGATAATTGCATT
EST: gi|166527000|gb|EG161905.1|EG161905
EST:     AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAA                         GCATTGCTAGAGGAATGGATAGACCAC
genomic: AGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgctt ... ttctgttcagGCATTGCTAGAGGAATGGATAG-CCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGACCAACAGAAGAATAATGCCACCAAGAAAGACAAACCTGCTGCTGAGCCGATAATTGTTCCAATTGTACTGAGGATGTCTGATTTTGATCACAAAgtgtgtgcttttgttggttttctaaagacatatctacctttatttttataacatacttttggttctataatgtctttgcaatatcatttgtaatttgtat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG