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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctctgtgatgattggtctcagtattgtactgggtttcagtgtgtctgctcagagtcttagcccgttgaatccatagtttgtctgtttttcaccaggaactgtataggatgttctctaaccaatggccaggccaatgctcattgtggtttgaaacctttgttcgatatatagtctgaactctgaattgatgcagAGAAGGCAGGAAAGAGCTAAAAAGATGGAAGAAAAGAAAGTGTATCTGCAACTATACGAAGCAATGGAGGCGTTGGTCAAGATCAATCTGGAGACGAACA

Basic information

species Zea mays
transcript GRMZM2G022909_T01
intron # 6
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|4647087|gb|AI622162.1|AI622162
EST:     CAGGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG                         AGAAGGCAGGAAAGAGCTAAAAAGATGGAAGAAAAGAAAGTGTATCTGCAA
genomic: CAGGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACGgtgagttctc ... attgatgcagAGAAGGCAGGAAAGAGCTAAAAAGATGGAAGAAAAGAAAGTGTATCTGCAA
EST: gi|83278406|gb|DV942414.1|DV942414
EST:     TATGAGTGCAGGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG                         AGAAGGCAGGAAAGAGCTAAGAAGATGGAAGAAAAGAAAGTGTATCTGCAA
genomic: TATGAGTGCAGGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACGgtgagttctc ... attgatgcagAGAAGGCAGGAAAGAGCTAAAAAGATGGAAGAAAAGAAAGTGTATCTGCAA
EST: gi|61117969|gb|DN558930.1|DN558930
EST:     TCTCTTGTCGAAGCTGATACG                         AGAAGGCAGGAAAGAGCTAAAAAGATGGAAGAAAAGAAAGTGTATCTGCAA
genomic: TCTCTTGTCGAAGCTGATACGgtgagttctc ... attgatgcagAGAAGGCAGGAAAGAGCTAAAAAGATGGAAGAAAAGAAAGTGTATCTGCAA
EST: gi|37380072|gb|CF626816.1|CF626816
EST:     TATGAGTGCAGGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG                         AGAAGGCAGGAAAGAGCTAAAAAGATGGAAGAAAAGAAAGTGTATCTGCAA
genomic: TATGAGTGCAGGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACGgtgagttctc ... attgatgcagAGAAGGCAGGAAAGAGCTAAAAAGATGGAAGAAAAGAAAGTGTATCTGCAA
EST: gi|61117970|gb|DN558931.1|DN558931
EST:     TCTCTTGTCGAAGCTGATACG                         AGAAGGCAGGAAAGAGCTAAAAAGATGGAAGAAAAGAAAGTGTATCTGCAA
genomic: TCTCTTGTCGAAGCTGATACGgtgagttctc ... attgatgcagAGAAGGCAGGAAAGAGCTAAAAAGATGGAAGAAAAGAAAGTGTATCTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgtggtttgaaacctttgttcgatatatagtctgaactctgaattgatgcagAGAAGGCAGGAAAGAGCTAAAAAGATGGAAGAAAAGAAAGTGTATCTGCAACTATACGAAGCAATGGAGGCGTTGGTCAAGATCAATCTGGAGACGAACA
                                            aattgat  putative branch site (score: 4)
                         atatatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttctctgtgatgattggtctcagtattgtactgggtttcagtgtgtctgctcagagtcttagcccgttgaatccatagtttgtctgtttttcaccaggaactgtataggatgttctctaaccaatggccaggccaatgctcattgtggtttgaaacctttgttcgatatatagtctgaactctgaattgatgcagAGAAGGCAGGAAAGAGCTAAAAAGATGGAAGAAAAGAAAGTGTATCTGCAACTATACGAAGCAATGGAGGCGTTGGTCAAGATCAATCTGGAGACGAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA