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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtataaaagtttttttgcttgccaattgatggccttcatctaatttctagatgtgtgtatggttgattcattcaattcttttatgcattttttcttgcagAATGAAAGCATTAAGGTATGCAGTTGGATATTGCATTCAGAGAGGCTCAAGCGATAGCTGCAAGTAGTTCTACCTTGTGCCCAGTTTTCTTGTTCTTTTA

Basic information

species Zea mays
transcript GRMZM2G111809_T02
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|50339117|gb|CO534243.1|CO534243
EST:     AATCTCGACAAGGGGCCACCTGTCGCTCTGGACAAGGGGGCTGCCCTAAG                         AATGAAAGCATTAAGGTATGCAGTTGGATATTGCATTCAGAGAGGCTCAAG
genomic: AATCTCGACAAGGGGCCACCTGTCGCTCTGGACAAGGGGGCTGCCCTAAGgtgattggtt ... tttcttgcagAATGAAAGCATTAAGGTATGCAGTTGGATATTGCATTCAGAGAGGCTCAAG
EST: gi|60341088|gb|DN208061.1|DN208061
EST:     AATCTCGACAAGGGGCCACCTGTCGCTCTGGACAAGGGGGCTGCCCTAAG                         AATGAAAGCATTAAGGTATGCAGTTGGATATTGCATTCAGAGAGGCTCAAG
genomic: AATCTCGACAAGGGGCCACCTGTCGCTCTGGACAAGGGGGCTGCCCTAAGgtgattggtt ... tttcttgcagAATGAAAGCATTAAGGTATGCAGTTGGATATTGCATTCAGAGAGGCTCAAG
EST: gi|211031526|gb|FL016975.1|FL016975
EST:     AATCTCGACAAGGGGCCACCTGTCGCTCTGGACAAGGGGGCTGCCCTAAG                         AATGAAAGCATTAAGGTATGCAGTTGGATATTGCATTCAGAGA
genomic: AATCTCGACAAGGGGCCACCTGTCGCTCTGGACAAGGGGGCTGCCCTAAGgtgattggtt ... tttcttgcagAATGAAAGCATTAAGGTATGCAGTTGGATATTGCATTCAGAGA
EST: gi|60341259|gb|DN208232.1|DN208232
EST:     AATCTCGACAAGGGGCCACCTGTCGCTCTGGACAAGGGGGCTGCCCTAAG                         AATGAAAGCATTAAGGTATGCAGTTGGATATTGCATTCAGAGAGGCTCAAG
genomic: AATCTCGACAAGGGGCCACCTGTCGCTCTGGACAAGGGGGCTGCCCTAAGgtgattggtt ... tttcttgcagAATGAAAGCATTAAGGTATGCAGTTGGATATTGCATTCAGAGAGGCTCAAG
EST: gi|60397812|gb|DN230628.1|DN230628
EST:     AATCTCGACAAGGGGCCACCTGTCGCTCTGGACAAGGGGGCTGCCCTAAG                         AATGAAAGCATTAAGGTATGCAGTTGGATATTGCATTCAGAGAGGCTCAAG
genomic: AATCTCGACAAGGGGCCACCTGTCGCTCTGGACAAGGGGGCTGCCCTAAGgtgattggtt ... tttcttgcagAATGAAAGCATTAAGGTATGCAGTTGGATATTGCATTCAGAGAGGCTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctagatgtgtgtatggttgattcattcaattcttttatgcattttttcttgcagAATGAAAGCATTAAGGTATGCAGTTGGATATTGCATTCAGAGAGGCTCAAGCGATAGCTGCAAGTAGTTCTACCTTGTGCCCAGTTTTCTTGTTCTTTTA
               ggttgat  putative branch site (score: 5)
                              ttcttttatgcatttt  putative PPT
                        attcaattcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaaagtttttttgcttgccaattgatggccttcatctaatttctagatgtgtgtatggttgattcattcaattcttttatgcattttttcttgcagAATGAAAGCATTAAGGTATGCAGTTGGATATTGCATTCAGAGAGGCTCAAGCGATAGCTGCAAGTAGTTCTACCTTGTGCCCAGTTTTCTTGTTCTTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC