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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgcttctctgttattttgaattaagcagcatgtctctgttctcaccagagagaaatttcagagaataacccgagttttcttttcccttgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACTGTGACCTTTATTAGATGTCTTTCCGCAGCATTGTGCGTGATGTAAGAGA

Basic information

species Zea mays
transcript GRMZM2G001272_T01
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|149077539|gb|EE166236.2|EE166236
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGGCAG                      
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGT-CC---CAGgtgcgtgtcg ... tgttagg
EST: gi|148981596|gb|EE027753.2|EE027753
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGGCAG                      
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGT-CC---CAGgtgcgtgtcg ... tgttagg
EST: gi|148955113|gb|EC900627.2|EC900627
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAG                         GCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGgtgcgtgtcg ... tgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
EST: gi|148965634|gb|EE016482.2|EE016482
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAG                         GCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGgtgcgtgtcg ... tgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
EST: gi|149111854|gb|EE191009.2|EE191009
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAG                         GCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGgtgcgtgtcg ... tgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
EST: gi|211530040|gb|FL043874.1|FL043874
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAG                         GCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGgtgcgtgtcg ... tgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
EST: gi|149029779|gb|EE286269.2|EE286269
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGGCAG                      
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGT-CC---CAGgtgcgtgtcg ... tgttagg
EST: gi|149044467|gb|EE047589.2|EE047589
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAG                         GCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGgtgcgtgtcg ... tgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
EST: gi|211530043|gb|FL043877.1|FL043877
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAG                         GCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGgtgcgtgtcg ... tgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
EST: gi|149101708|gb|EE187845.2|EE187845
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAG                         GCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGgtgcgtgtcg ... tgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
EST: gi|211530044|gb|FL043878.1|FL043878
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGGCAG                      
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGT-CC---CAGgtgcgtgtcg ... tgttagg
EST: gi|149074592|gb|EE162995.2|EE162995
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAG                         GCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGgtgcgtgtcg ... tgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
EST: gi|78085094|gb|DV513487.1|DV513487
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAG                         GCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGgtgcgtgtcg ... tgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
EST: gi|149076331|gb|EE164946.2|EE164946
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGGCAG                      
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGT-CC---CAGgtgcgtgtcg ... tgttagg
EST: gi|148945477|gb|EC890712.2|EC890712
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGGCAG                      
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGT-CC---CAGgtgcgtgtcg ... tgttagg
EST: gi|50333305|gb|CO528431.1|CO528431
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAG                         GCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGgtgcgtgtcg ... tgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
EST: gi|148940279|gb|EC885058.2|EC885058
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAG                         GCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGgtgcgtgtcg ... tgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACT
EST: gi|149014539|gb|EE044173.2|EE044173
EST:     GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGTCCCAGGCAG                      
genomic: GCAGCCCGCGCCGCTCGGCCTCCCGTAGCCGACGCCCGGCCCCGT-CC---CAGgtgcgtgtcg ... tgttagg


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccagagagaaatttcagagaataacccgagttttcttttcccttgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACTGTGACCTTTATTAGATGTCTTTCCGCAGCATTGTGCGTGATGTAAGAGA
                    gaataac  putative branch site (score: 2)
                                ttttcttttcccttgt  putative PPT
                                ttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgcttctctgttattttgaattaagcagcatgtctctgttctcaccagagagaaatttcagagaataacccgagttttcttttcccttgttaggcagGCTCATCTTTGCACAGAGTCATTGGAGGAAGTTTGATGTTTCAGCAGTACTGTGACCTTTATTAGATGTCTTTCCGCAGCATTGTGCGTGATGTAAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA