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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaatattttgggtaagttcaaagcttgaactgaaatagagagaggagtgtgtaacctagtgtcaaatacctcctcaataaagatatgcttgtcagtagGTGACAACTCAAGATCAGCAGGCATAATGTCACTCAGTAGATTGTGTGTATATGGATCATCATCTATCACCTATGTGCTCTCCGCCCGCGGAACTTCAGG

Basic information

species Zea mays
transcript GRMZM2G466549_T02
intron # 4
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|26456347|gb|CA827930.1|CA827930
EST:     TCGGCAGTACTTTGCTGGTAGCCTAAAAGATGCAGCAAGGAGCCTTGGAG                         GTGACAACTCAAGATCAGCAGGCATAATGTCACTCAGTAGATTGTGTGTAT
genomic: TCGGCAGTACTTTGCTGGTAGCCTAAAAGATGCAGCAAGGAGCCTTGGAGgtgagtgaat ... ttgtcagtagGTGACAACTCAAGATCAGCAGGCATAATGTCACTCAGTAGATTGTGTGTAT
EST: gi|87157376|gb|DY402165.1|DY402165
EST:     TCGGCAGTACTTTGCTGGTAGCCTAAAAGATGCAGCAAGGAGCCTTGGAG                         GTGACAACTCAAGATCAGCAGGCATAATGTCACTCAGTAGATTGTGTGTAT
genomic: TCGGCAGTACTTTGCTGGTAGCCTAAAAGATGCAGCAAGGAGCCTTGGAGgtgagtgaat ... ttgtcagtagGTGACAACTCAAGATCAGCAGGCATAATGTCACTCAGTAGATTGTGTGTAT
EST: gi|22935650|gb|BU571925.1|BU571925
EST:     TCGGCAGTACTTTGCTGGTAGCCTAAAAGATGCAGCAAGGAGCCTTGGAG                         GTGACAACTCAAGATCAGCAGGCATAATGTCACTCAGTAGATTGTGTGTAT
genomic: TCGGCAGTACTTTGCTGGTAGCCTAAAAGATGCAGCAAGGAGCCTTGGAGgtgagtgaat ... ttgtcagtagGTGACAACTCAAGATCAGCAGGCATAATGTCACTCAGTAGATTGTGTGTAT
EST: gi|20507543|gb|BQ279677.1|BQ279677
EST:     GCCTAAAAGATGCAGCAAGGAGCCTTGGAG                         GTGACAACTCAAGATCAGCAGGCATAATGTCACTCAGTGAGATTGTGTGTA
genomic: GCCTAAAAGATGCAGCAAGGAGCCTTGGAGgtgagtgaat ... ttgtcagtagGTGACAACTCAAGATCAGCAGGCATAATGTCACTCAGT-AGATTGTGTGTA
EST: gi|26559361|gb|CA831596.1|CA831596
EST:     TCGGCAGTACTTTGCTGGTAGCCTAAAAGATGCAGCAAGGAGCCTTGGAG                         GTGACAACTCAAGATCAGCAGGCATAATGTCACTCAGTAGATTGTGTGTAT
genomic: TCGGCAGTACTTTGCTGGTAGCCTAAAAGATGCAGCAAGGAGCCTTGGAGgtgagtgaat ... ttgtcagtagGTGACAACTCAAGATCAGCAGGCATAATGTCACTCAGTAGATTGTGTGTAT
EST: gi|20802834|gb|BQ293884.1|BQ293884
EST:     GGAGCCTTGGAG                         GTGACAACTCAAGATCAGCAAGGCATAATGTCACTCAGTAGATTG-GTGTA
genomic: GGAGCCTTGGAGgtgagtgaat ... ttgtcagtagGTGACAACTCAAGATCAGC-AGGCATAATGTCACTCAGTAGATTGTGTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagtgtgtaacctagtgtcaaatacctcctcaataaagatatgcttgtcagtagGTGACAACTCAAGATCAGCAGGCATAATGTCACTCAGTAGATTGTGTGTATATGGATCATCATCTATCACCTATGTGCTCTCCGCCCGCGGAACTTCAGG
     gtgtaac  putative branch site (score: 3)
                                aataaagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaatattttgggtaagttcaaagcttgaactgaaatagagagaggagtgtgtaacctagtgtcaaatacctcctcaataaagatatgcttgtcagtagGTGACAACTCAAGATCAGCAGGCATAATGTCACTCAGTAGATTGTGTGTATATGGATCATCATCTATCACCTATGTGCTCTCCGCCCGCGGAACTTCAGG

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