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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtccaccatcaccaccaaaaatcttcagggaattcgatgacgtggcagctgcccccagtgtggctaaatagaaattttccgtattcattgcagGATACATCCGATTGCTGCGGTGTGTTAAAACAGCAGTACGGTGTGCTTCTGCGGGAGAAGGAGGAATGCAGGAGGCTGTTAGAGGACCTCATGAGGGAGA

Basic information

species Zea mays
transcript GRMZM2G400223_T01
intron # 2
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|78124570|gb|DV542954.1|DV542954
EST:     GCGGTGGTCGAGCCCTCCCAGGGGGCCCGCAACCGGAAGAGTCTGGAGAG                         GATACATCCGATTGCTGCGGTGTGTTAAAACAGCAGTACGGTGTGCTTCTG
genomic: GCGGTGGTCGAGCCGTCCCAGGGGGCCCGCAACCGGAAGAGTCTGGAGAGgttgtccacc ... ttcattgcagGATACATCCGATTGCTGCGGTGTGTTAAAACAGCAGTACGGTGTGCTTCTG
EST: gi|31663986|gb|CD573166.1|CD573166
EST:     CGCAACCGGAA-A-TCTGGAGAG                         GATACATCCGATTGCTGCGG-GTGTTAAAACAGCAGTACGG-GTGCTTCTG
genomic: CGCAACCGGAAGAGTCTGGAGAGgttgtccacc ... ttcattgcagGATACATCCGATTGCTGCGGTGTGTTAAAACAGCAGTACGGTGTGCTTCTG
EST: gi|31664597|gb|CD573530.1|CD573530
EST:     CAACCGGAAGAGTCTGGAGAG                         GATACATCCGATTGCTGCGG-GTGTTAAAACAGCAGTACGGTGTGCTTCTG
genomic: CAACCGGAAGAGTCTGGAGAGgttgtccacc ... ttcattgcagGATACATCCGATTGCTGCGGTGTGTTAAAACAGCAGTACGGTGTGCTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacgtggcagctgcccccagtgtggctaaatagaaattttccgtattcattgcagGATACATCCGATTGCTGCGGTGTGTTAAAACAGCAGTACGGTGTGCTTCTGCGGGAGAAGGAGGAATGCAGGAGGCTGTTAGAGGACCTCATGAGGGAGA
                       ggctaaa  putative branch site (score: 3)
                          taaatagaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtccaccatcaccaccaaaaatcttcagggaattcgatgacgtggcagctgcccccagtgtggctaaatagaaattttccgtattcattgcagGATACATCCGATTGCTGCGGTGTGTTAAAACAGCAGTACGGTGTGCTTCTGCGGGAGAAGGAGGAATGCAGGAGGCTGTTAGAGGACCTCATGAGGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA