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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attctatggttcactacacaatttgcattattttgtcttgtctcctttgcttcttcacctatctgacattattttctttctttgtatgtttccagttcagGAGACATCTTCGAGAAGCTGAAATGGCTCCTAAAG

Basic information

species Zea mays
transcript GRMZM2G083253_T04
intron # 1
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|60343365|gb|DN210338.1|DN210338
EST:     CGCGTCCGCCTCAGCCCGCCGCAAGGAGAGGTAAG                     
genomic: CGCGTCCGCCTCAGCCCGCCGCAA-G-GA-G--AGgtaaggtaag ... tccagt
EST: gi|211347545|gb|FL350551.1|FL350551
EST:     AGCCGTCATCGTTTCGCGTCTGCCTCAGCCCGCCGCAAGAGAGGTAAG                         GAGACATCTTCGAGAAGCTGAAATGGCTCCTAAAG
genomic: AGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAAG-GA-G--AGgtaaggtaag ... tccagttcagGAGACATCTTCGAGAAGCTGAAATGGCTCCTAAAG
EST: gi|32915548|gb|CF020360.1|CF020360
EST:     CCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAAGGAGAGGTAAGTTCAG                
genomic: CCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGC----A-AGG--AG---AGgtaaggtaag ... t
EST: gi|76928741|gb|DV171747.1|DV171747
EST:     TTCGCGTCCGCCTCAGCCCGCCGCAAGGAGAGTTCAG                     
genomic: TTCGCGTCCGCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|211369284|gb|FK958224.1|FK958224
EST:     AGCCGTCATCGTTTCGCGTCTGCCTCAGCCCGCCGCAAGGAGAG                         GAGACATCTTCGAGAAGCTGAAATGGCTCCTAAAG
genomic: AGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAAGGAGAGgtaaggtaag ... tccagttcagGAGACATCTTCGAGAAGCTGAAATGGCTCCTAAAG
EST: gi|211211590|gb|FL253350.1|FL253350
EST:     TCCCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAAGGAGAGTTCAG                     
genomic: TCCCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|211211579|gb|FL253339.1|FL253339
EST:     TCCCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCACCGCAAGGAGAGTTCAG                     
genomic: TCCCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|211206438|gb|FL253313.1|FL253313
EST:     TCCCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCACCGCAAGGAGAGTTCAG                     
genomic: TCCCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|211214151|gb|FL253355.1|FL253355
EST:     CCAGCCGTCATCGTTTCGCGTCTGCCTCAGCCCGCCGCAAGAGAGTTCAG                         GAGACATCTTCGAGAAGCTGAAATGGCTCCTAAAG
genomic: CCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAAG-GAG---AGgtaaggtaag ... tccagttcagGAGACATCTTCGAGAAGCTGAAATGGCTCCTAAAG
EST: gi|211209013|gb|FL253324.1|FL253324
EST:     CCCAGCCGTCATCGTTTCGCGTCTGCCTCAGCCCGCCGCAAGGAGAGTTCAG                     
genomic: CCCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|211209020|gb|FL253331.1|FL253331
EST:     CCCAGCCGTCATCGTTTCGCGTCTGCCTCAGCCCGCCGCAAGGAGAGGTAAG                     
genomic: CCCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAA-G-GA-G--AGgtaaggtaag ... tccagt
EST: gi|60354314|gb|DN221287.1|DN221287
EST:     CGTCCGCCTCAGCCCGCCGCAAGGAGAGTTCAG                     
genomic: CGTCCGCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|60355240|gb|DN222213.1|DN222213
EST:     TCGCGTCCGCCTCAGCCCGCCGCAAGGAGAGTTCAG                     
genomic: TCGCGTCCGCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|211158896|gb|FL336036.1|FL336036
EST:     CCAGCCGTCATCGTTTCGCGTCTGCCTCAGCCCGCCGCAAGAGAGGTAAG                         GAGACATCTTCGAGAAGCTGAAATGGCTCCTAAAG
genomic: CCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAAG-GA-G--AGgtaaggtaag ... tccagttcagGAGACATCTTCGAGAAGCTGAAATGGCTCCTAAAG
EST: gi|211214155|gb|FL253359.1|FL253359
EST:     CCCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAAGGAGAGTTCAG                     
genomic: CCCAGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|29577083|gb|CB617195.1|CB617195
EST:     TCAGCCCGCCGCAAGGAGAGTTCAG                     
genomic: TCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|211203871|gb|FL253303.1|FL253303
EST:     AGCCGTCATCGTTTCGCGTCTGCCTCAGCCCGCCGCAAGGAGAGTTCAG                     
genomic: AGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|32917834|gb|CF022646.1|CF022646
EST:     AGCCGTCATCGTTTCGCGTGCGCCTCAGCCCGCCGCAAGGAGAGTTCAG                     
genomic: AGCCGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|67022151|gb|CO450900.1|CO450900
EST:     CATCGTTTCGCGTCCGCCTCAGCCCGCCGCAAGGAGAGGTAAGTTCAG                
genomic: CATCGTTTCGCGTCCGCCTCAGCCCGCCGC----A-AGG--AG---AGgtaaggtaag ... t
EST: gi|29947455|gb|CB816665.1|CB816665
EST:     GTTTCGCGTCCGCCTCAGCCCGCCGCAAGGAGAGTTCAG                     
genomic: GTTTCGCGTCCGCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|211214159|gb|FL253363.1|FL253363
EST:     CGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAAGGAGAGTTCAG                     
genomic: CGTCATCGTTTCGCGTCCGCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|60339950|gb|DN206923.1|DN206923
EST:     GCCTCAGCCCGCCGCAAGGAGAGTTCAG                     
genomic: GCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt
EST: gi|31612058|gb|CD568680.1|CD568680
EST:     GTTTCGCGTCCGCCTCAGCCCGCCGCAAGGAGAGTTCAG                     
genomic: GTTTCGCGTCCGCCTCAGCCCGCCGCAA-G-GAG---AGgtaaggtaag ... tccagt


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcttcttcacctatctgacattattttctttctttgtatgtttccagttcagGAGACATCTTCGAGAAGCTGAAATGGCTCCTAAAG
               atctgac  putative branch site (score: 3)
                          ttttctttctttgtat  putative PPT
                      attattttctttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attctatggttcactacacaatttgcattattttgtcttgtctcctttgcttcttcacctatctgacattattttctttctttgtatgtttccagttcagGAGACATCTTCGAGAAGCTGAAATGGCTCCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - -cactaca
- - - - - - - - - - - ttgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtatg