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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgaatacctgttgtgggcagaaagcctgaaagaatgcttgtcctgttgtttcatacatatctttgtttctttagtcatcattttttttcttttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT

Basic information

species Zea mays
transcript GRMZM5G863152_T01
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|211223994|gb|FL296362.1|FL296362
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATG
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATG
EST: gi|211226059|gb|FL296375.1|FL296375
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATG
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATG
EST: gi|211226060|gb|FL296376.1|FL296376
EST:     ATTAAAGAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATG
genomic: ATTAAA-AGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAATG
EST: gi|211135925|gb|FL188995.1|FL188995
EST:     ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAG                         TGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
genomic: ATTAAAAGCAAGAAGAGGCGAAAGGATGTTGCACTGGAATCAAGgtactctcct ... tttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttcatacatatctttgtttctttagtcatcattttttttcttttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT
                                            ttttgat  putative branch site (score: 4)
              tctttgtttctttagt  CT-rich tract
                               atcattttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgaatacctgttgtgggcagaaagcctgaaagaatgcttgtcctgttgtttcatacatatctttgtttctttagtcatcattttttttcttttgatgtagTGAGGTAATATCTGGAAATCCAAGGAACAGGGACCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA