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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggcatatctgccgttccaaagcatacaggctgaatttctcggctgattattctagcttgccttccttctctcattttttaacgtttattttctaatagttgggtatggatccacagCAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTGAACCTCGCTTCGTCGATCAATAAGATAAATAGATAATTCCCAGCTGCTA

Basic information

species Zea mays
transcript GRMZM2G090647_T04
intron # 8
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|47962698|gb|CN845407.1|CN845407
EST:     AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAG                         CAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTG
genomic: AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAGgtgaggcata ... ggatccacagCAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTG
EST: gi|5686889|gb|AI939803.1|AI939803
EST:     AATCTGAGACTGGAGGAGGTTTNTGGCATGTGGAGTAGACATCATCCAAG                         CAGAGCTAGAGAAGCGGAAGCTGG
genomic: AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAGgtgaggcata ... ggatccacagCAGAGCTAGAGAAGCGGAAGCTGG
EST: gi|71770109|gb|DR968046.1|DR968046
EST:     AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAG                         CAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTG
genomic: AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAGgtgaggcata ... ggatccacagCAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTG
EST: gi|30705964|gb|CD058985.1|CD058985
EST:     AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAG                         CAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTG
genomic: AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAGgtgaggcata ... ggatccacagCAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTG
EST: gi|76918843|gb|DV167481.1|DV167481
EST:     AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAG                         -AG--CTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTG
genomic: AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAGgtgaggcata ... ggatccacagCAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTG
EST: gi|5018209|gb|AI714402.1|AI714402
EST:     AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAG                         CAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTG
genomic: AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAGgtgaggcata ... ggatccacagCAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTG
EST: gi|211242536|gb|FL481660.1|FL481660
EST:     AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAG                         -AG--CTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTG
genomic: AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAGgtgaggcata ... ggatccacagCAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTG
EST: gi|211164192|gb|FL363087.1|FL363087
EST:     AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAG                         -AG--CTAGAGAAGCGGAA-CTSGGTACTGCGTTGCCTGAAAGCAAATTTG
genomic: AATCTGAGACTGGAGGAGGTTTCTCGCATGTGGAGTAGACATCATACAAGgtgaggcata ... ggatccacagCAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttctctcattttttaacgtttattttctaatagttgggtatggatccacagCAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTGAACCTCGCTTCGTCGATCAATAAGATAAATAGATAATTCCCAGCTGCTA
                            ttctaat  putative branch site (score: 2)
           attttttaacgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggcatatctgccgttccaaagcatacaggctgaatttctcggctgattattctagcttgccttccttctctcattttttaacgtttattttctaatagttgggtatggatccacagCAGAGCTAGAGAAGCGGAAGCTGGGTACTGCGTTGCCTGAAAGCAAATTTGAACCTCGCTTCGTCGATCAATAAGATAAATAGATAATTCCCAGCTGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT