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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcaggcgtccatagtaaatgaaattggtgcatatatttgagttgactaacaatgcgataactaacatgtgatttgtcgattttcctttttactgctagATTTTGAGCCCAACAATCTCGCTGCCACCGATACTCCTGGTTCGTATATTTGGTTACTCAAAACATGAGATGATCCTCTGAAGTAGAAAGGGAAACACTG

Basic information

species Zea mays
transcript GRMZM2G480607_T06
intron # 11
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|211196286|gb|FL474590.1|FL474590
EST:     CCTGACAGTGGAGCAGAAATTCATTAAGAGCATATAGGGATTCACAAGTG                         ATTTTGAGCCCAACAATCTCGCTGCCACCGATACTNCCTGGTTCGTATATT
genomic: CCTGACAGTGGAGCAGAAATTCATTAAGAGCATATAGGGATTCACAAGTGgtacatgtat ... ttactgctagATTTTGAGCCCAACAATCTCGCTGCCACCGATACT-CCTGGTTCGTATATT
EST: gi|211196285|gb|FL474589.1|FL474589
EST:     CCTGACAGTGGAGCAGAAATTCATTAAGAGCATATAGGGATTCACAAGTG                         ATTTTGAGCCCAACAATCTCGCTGCCACCGATACTCCTGGTTCGTATATTT
genomic: CCTGACAGTGGAGCAGAAATTCATTAAGAGCATATAGGGATTCACAAGTGgtacatgtat ... ttactgctagATTTTGAGCCCAACAATCTCGCTGCCACCGATACTCCTGGTTCGTATATTT
EST: gi|71761611|gb|DR959548.1|DR959548
EST:     CCTGACAGTGGAGCAGAAATTCATTAAGAGCATATAGGGATTCACAAGTG                         ATTTTGAGCCCAACAATCTCGCTGCCACCGATACTCCTGGTTCGTATATTT
genomic: CCTGACAGTGGAGCAGAAATTCATTAAGAGCATATAGGGATTCACAAGTGgtacatgtat ... ttactgctagATTTTGAGCCCAACAATCTCGCTGCCACCGATACTCCTGGTTCGTATATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactaacaatgcgataactaacatgtgatttgtcgattttcctttttactgctagATTTTGAGCCCAACAATCTCGCTGCCACCGATACTCCTGGTTCGTATATTTGGTTACTCAAAACATGAGATGATCCTCTGAAGTAGAAAGGGAAACACTG
               aactaac  putative branch site (score: 1)
                                    ttttcctttttactgc  putative PPT
             ataactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcaggcgtccatagtaaatgaaattggtgcatatatttgagttgactaacaatgcgataactaacatgtgatttgtcgattttcctttttactgctagATTTTGAGCCCAACAATCTCGCTGCCACCGATACTCCTGGTTCGTATATTTGGTTACTCAAAACATGAGATGATCCTCTGAAGTAGAAAGGGAAACACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG