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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggctactgaaataatctctagtattatgtagctgtgccttttgtcttgtaatgctctgactgattctctttctggcttccttaaactccttttgcagGCCCCGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGTCCT

Basic information

species Zea mays
transcript GRMZM2G039889_T05
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|148952088|gb|EC897879.2|EC897879
EST:     CGACGTCGGCGCCTTCGACTCGTATGTCGGCGCGAGACGATCCGCGGAAG                         GCCCCGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGT
genomic: CGACGTCGGCGCCTTCGACTCGTATGTCGGCGCGAGACGATCCGCGGAAGgtgagagctg ... ccttttgcagGCCCCGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGT
EST: gi|211416501|gb|FL082404.1|FL082404
EST:     CGACGTCGGCGCCTTCGACTCGTATGTCGGCGCGAGACGATCCGCGGAAG                         GCCCCGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGT
genomic: CGACGTCGGCGCCTTCGACTCGTATGTCGGCGCGAGACGATCCGCGGAAGgtgagagctg ... ccttttgcagGCCCCGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGT
EST: gi|91052439|gb|EB162857.1|EB162857
EST:     CGACGTCGGCGCCTTCGACTCGTATGTCGGCGCGAGACGATCCGCGGAAG                         GCCCCGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGT
genomic: CGACGTCGGCGCCTTCGACTCGTATGTCGGCGCGAGACGATCCGCGGAAGgtgagagctg ... ccttttgcagGCCCCGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttgtaatgctctgactgattctctttctggcttccttaaactccttttgcagGCCCCGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGTCCT
               gactgat  putative branch site (score: 3)
                                           ctccttttgc  putative PPT
                                      ttaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggctactgaaataatctctagtattatgtagctgtgccttttgtcttgtaatgctctgactgattctctttctggcttccttaaactccttttgcagGCCCCGAATGTTGAAGATTCTTATCCTGAGCGACCAGGGGAACCAGATTGTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA