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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgttctttaccatggcttcataaccgaatagtccaagtgttttactggtttctttgatgtagagttcattgtcttcatataccgattatttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCTTGCTGCAGTTGTTAATCAATACATTGCAAAACTAGTAAAAGAATTACAA

Basic information

species Zea mays
transcript GRMZM2G128080_T02
intron # 3
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|6626347|gb|AW257879.1|AW257879
EST:     AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
EST: gi|149042519|gb|EE047203.2|EE047203
EST:     AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
EST: gi|76286839|gb|DV026407.1|DV026407
EST:     AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
EST: gi|101382451|gb|EB813281.1|EB813281
EST:     AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
EST: gi|148938451|gb|EC882769.2|EC882769
EST:     AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
EST: gi|211362118|gb|FL332260.1|FL332260
EST:     AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
EST: gi|211158653|gb|FK974899.1|FK974899
EST:     AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
EST: gi|211185838|gb|FL326885.1|FL326885
EST:     AGTCGGGATATTACCATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
EST: gi|211134103|gb|FL315808.1|FL315808
EST:     AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
EST: gi|211314481|gb|FL348235.1|FL348235
EST:     AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
EST: gi|211477295|gb|FL319648.1|FL319648
EST:     AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
EST: gi|211439800|gb|FL306622.1|FL306622
EST:     AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
EST: gi|71328613|gb|DR800971.1|DR800971
EST:     AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
EST: gi|15499422|gb|BI595935.1|BI595935
EST:     AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAG                         AATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT
genomic: AGTCGGGATATTACAATGAACAGCAAAAAGGTCATCTTTCAGGTCCACAGgtaagcagtg ... tttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actggtttctttgatgtagagttcattgtcttcatataccgattatttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCTTGCTGCAGTTGTTAATCAATACATTGCAAAACTAGTAAAAGAATTACAA
        ctttgat  putative branch site (score: 5)
                                             tttgtttc  putative PPT
                                         attatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgttctttaccatggcttcataaccgaatagtccaagtgttttactggtttctttgatgtagagttcattgtcttcatataccgattatttgtttcagAATCACGAAAGTTAACAGGGACGAAGTTCTCTCGAAGGCAGAAAATGATCTTGCTGCAGTTGTTAATCAATACATTGCAAAACTAGTAAAAGAATTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA