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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataattagttctctgagaacattttcgattttgatatagctgctttgtatttttcccaataccaaatagaaaaaaataccgttatactttgtttcaactaatctcagtttgttgaacatgctcccttttcatttattatagGAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG

Basic information

species Zea mays
transcript GRMZM2G325131_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G325131_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g38950.3 (Oryza sativa), 3'ss of exon 3
gtataattagttctctgagaacattttcgattttgatatagctgctttgtatttttcccaataccaaatagaaaaaaataccgttatactttgtttcaactaatctcagtttgttga--acatgctcccttttcatttattatagGAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG--------------------------------------------------------------
      |   ||||  ||| |||| |||  || |||| ||   |       ||  | |    ||||||   |||  |      |||| | | ||   ||||  ||||||| |  |||    |  |||   ||| || |  | ||||||||||||||| |||||||||||||||||||| ||||                                                              
-----gtattttcttggagcacatattcatttgtgatttattag-------ttgcttcatgcaccaaaggaaaagga------ttatgcat-gtaataact--tctcagtgttctgatggtaatctcatatttaatcttctgtagGAAGAACCCAAGAGGAATACTTATTTCTCCAGGGCCTGGTAAGTTTGTCTTGTGAATATCATGACAGTAAATACAGTATATAGGCCTGAGTGTAACAATT

upper sequence: GRMZM2G325131_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g38950.1 (Oryza sativa), 3'ss of exon 3
gtataattagttctctgagaacattttcgattttgatatagctgctttgtatttttcccaataccaaatagaaaaaaataccgttatactttgtttcaactaatctcagtttgttgaacatgctccctt--ttcatttattatagGAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG
      |   ||||  ||| |||| |||  || |||| ||   |       ||  | |    ||||||   |||  |      |||| | | ||   ||||  ||||||| |  |||   |  || | |  || || |  | ||||||||||||||| |||||||||||||||||||| ||||
-----gtattttcttggagcacatattcatttgtgatttattag-------ttgcttcatgcaccaaaggaaaagga------ttatgcat-gtaataact--tctcagtgttctgatggtaatctcatatttaatcttctgtagGAAGAACCCAAGAGGAATACTTATTTCTCCAGGGCCTG
















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|33099524|gb|CF059484.1|CF059484
EST:     AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAG                         GAAGAACCCAAGGGGAATACTTATTTCTCCCAGGACCTG
genomic: AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAGgtataattag ... tttattatagGAAGAACCCAAGGGGAATACTTATTTCT-CCAGGACCTG
EST: gi|33099031|gb|CF058991.1|CF058991
EST:     AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAG                         GAAGAACCCAAGGGGAATACTTATTTCTCCCAGGACCTG
genomic: AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAGgtataattag ... tttattatagGAAGAACCCAAGGGGAATACTTATTTCT-CCAGGACCTG
EST: gi|33100076|gb|CF060036.1|CF060036
EST:     AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAG                         GAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG
genomic: AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAGgtataattag ... tttattatagGAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG
EST: gi|33099556|gb|CF059516.1|CF059516
EST:     AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAG                         GAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG
genomic: AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAGgtataattag ... tttattatagGAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG
EST: gi|33100338|gb|CF060298.1|CF060298
EST:     AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAG                         GAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG
genomic: AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAGgtataattag ... tttattatagGAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG
EST: gi|33099441|gb|CF059401.1|CF059401
EST:     AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAG                         GAAGAACCCAAGGGGAATGCTTATTTCTCCAGGACCTG
genomic: AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAGgtataattag ... tttattatagGAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG
EST: gi|33099508|gb|CF059468.1|CF059468
EST:     AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAG                         GAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG
genomic: AACTTCGAAGTATACCGCAATGATGAACTGACCATAGAAGATGTGAGAAGgtataattag ... tttattatagGAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgtttcaactaatctcagtttgttgaacatgctcccttttcatttattatagGAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG
         aactaat  putative branch site (score: 2)
                                  ctcccttttcatttat  putative PPT
                                       ttttcatttattata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataattagttctctgagaacattttcgattttgatatagctgctttgtatttttcccaataccaaatagaaaaaaataccgttatactttgtttcaactaatctcagtttgttgaacatgctcccttttcatttattatagGAAGAACCCAAGGGGAATACTTATTTCTCCAGGACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC