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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatttctaatatgtcaatttaacatatccttaactgccttcattttggcttactatcagcagtctaggcaacttatagtgcatgcattgttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAGAGAAAGGCATGTCCATGATAGAGATAGGGACTATCGTCGTCGGAGCAGA

Basic information

species Zea mays
transcript GRMZM2G110143_T01
intron # 5
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|149005363|gb|EE039915.2|EE039915
EST:     GGGGGTGGGAAATCAAGAGACAGGTCAAGGAGCGGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|211440859|gb|FL253848.1|FL253848
EST:     GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|78076982|gb|DV505416.1|DV505416
EST:     GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|32846542|gb|CD986223.1|CD986223
EST:     GGGGTTGAGAAATCAAGAGACAGGTCAAGGGGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|71325766|gb|DR799564.1|DR799564
EST:     GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|50335676|gb|CO530802.1|CO530802
EST:     GAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|74237053|gb|DT644967.1|DT644967
EST:     AAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: AAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|50328941|gb|CO524067.1|CO524067
EST:     GTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|74241217|gb|DT649131.1|DT649131
EST:     GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTTCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|32833902|gb|CD973580.1|CD973580
EST:     GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|33100333|gb|CF060293.1|CF060293
EST:     GGGGTTGAGAAATCAAGAGCCAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|89247003|gb|DY618789.1|DY618789
EST:     TCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: TCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
EST: gi|76290039|gb|DV029607.1|DV029607
EST:     GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG                         GCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG
genomic: GGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggcttactatcagcagtctaggcaacttatagtgcatgcattgttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAGAGAAAGGCATGTCCATGATAGAGATAGGGACTATCGTCGTCGGAGCAGA
  ggcttac  putative branch site (score: 3)
                                          ttgtttt  putative PPT
                                         attgttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatttctaatatgtcaatttaacatatccttaactgccttcattttggcttactatcagcagtctaggcaacttatagtgcatgcattgttttaactagGCACAGAGACAGAGATGATAGAAGGCGAAGTCGCAGCAGGAGCAGGAGCAGAGAAAGGCATGTCCATGATAGAGATAGGGACTATCGTCGTCGGAGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG