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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgattataccttcatataattatggaacttagttgatacacttggcaggcaaactatatccagtatatgtaggattaattgttaagatggtcatctattttgtagGTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCACGACCTCTGCCCTTCTCTAGTAATTTCAGAGATGCCACTGTCAGAAGTG

Basic information

species Zea mays
transcript GRMZM2G133757_T01
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|74240369|gb|DT648283.1|DT648283
EST:     TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAG                         GTTCTTTTGCCAAGAGAACATTTAGAGAAACAATGTTCTTATGATGCTGCA
genomic: TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAGgtaaatgatt ... tattttgtagGTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCA
EST: gi|74237046|gb|DT644960.1|DT644960
EST:     TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAG                         GTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCA
genomic: TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAGgtaaatgatt ... tattttgtagGTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCA
EST: gi|91051391|gb|EB161809.1|EB161809
EST:     TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAG                         GTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCA
genomic: TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAGgtaaatgatt ... tattttgtagGTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCA
EST: gi|76289049|gb|DV028617.1|DV028617
EST:     TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAG                         GTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCA
genomic: TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAGgtaaatgatt ... tattttgtagGTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCA
EST: gi|78110369|gb|DV528781.1|DV528781
EST:     TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAG                         GTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCA
genomic: TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAGgtaaatgatt ... tattttgtagGTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCA
EST: gi|76285618|gb|DV025186.1|DV025186
EST:     TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAG                         GTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCA
genomic: TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAGgtaaatgatt ... tattttgtagGTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCA
EST: gi|101395524|gb|EB819690.1|EB819690
EST:     TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAG                         GTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCA
genomic: TGAAGCAGTCTGCTGTTGATTACTTGAATGGATCTGATTATGCATCTCAGgtaaatgatt ... tattttgtagGTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactatatccagtatatgtaggattaattgttaagatggtcatctattttgtagGTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCACGACCTCTGCCCTTCTCTAGTAATTTCAGAGATGCCACTGTCAGAAGTG
                      gattaat  putative branch site (score: 3)
                                           tctatttt  putative PPT
                       attaattgttaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgattataccttcatataattatggaacttagttgatacacttggcaggcaaactatatccagtatatgtaggattaattgttaagatggtcatctattttgtagGTTCTTTTGCCAAGAGAACATCTAGAGAAACAATGTTCTTATGATGCTGCACGACCTCTGCCCTTCTCTAGTAATTTCAGAGATGCCACTGTCAGAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT