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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccacaatgccatttggaaatgaaatctttccttggtttactggcatatttactaggaaatataagttctgagaataatttgctttaaagtagaattattgtttgtgcttgtcttttatatgtttgatcacatcattacacctccccccttccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG

Basic information

species Zea mays
transcript GRMZM2G172322_T02
intron # 9
splice site 3'
intron type U2

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|149037276|gb|EE155319.2|EE155319
EST:     TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAG                         GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
EST: gi|211393001|gb|FL405406.1|FL405406
EST:     TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGT-CTACAGATCAN                         GTAGA-TCTAAAGATGAGGTTGTAAGTA-GCAGTAGA
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGA
EST: gi|60359695|gb|DN226668.1|DN226668
EST:     TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAG                         GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
EST: gi|211356738|gb|FL440505.1|FL440505
EST:     TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAG                         GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
EST: gi|148956137|gb|EC901907.2|EC901907
EST:     TCCCAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTTTACAGATCAG                         GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
EST: gi|149101004|gb|EE187101.2|EE187101
EST:     TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAG                         GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
EST: gi|71319218|gb|DR796369.1|DR796369
EST:     TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAG                         GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
EST: gi|76285084|gb|DV024652.1|DV024652
EST:     TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAG                         GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
EST: gi|93017205|gb|EB642725.1|EB642725
EST:     TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAG                         GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
EST: gi|211356737|gb|FL440504.1|FL440504
EST:     TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAG                         GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
EST: gi|211428017|gb|FL465135.1|FL465135
EST:     TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAG                         GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
EST: gi|211428077|gb|FL466325.1|FL466325
EST:     TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTYTACAGATCAG                         GTAGAATYTAAAGATGAGGTTGTAAGTAAGCAGTAGATACCATTTTTTCCT
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
EST: gi|76932106|gb|DV172946.1|DV172946
EST:     TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAG                         GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
EST: gi|60398346|gb|DN231162.1|DN231162
EST:     TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAG                         GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT
genomic: TCACAATGAGGAGCCCGACTAGAAAAATTCGAAAAAGTTCTACAGATCAGgtccacaatg ... ccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgtcttttatatgtttgatcacatcattacacctccccccttccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG
               gtttgat  putative branch site (score: 5)
                          tcattacacctccccc  putative PPT
       ttttatatgtttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccacaatgccatttggaaatgaaatctttccttggtttactggcatatttactaggaaatataagttctgagaataatttgctttaaagtagaattattgtttgtgcttgtcttttatatgtttgatcacatcattacacctccccccttccaatttcagGTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG