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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgtagtttacttaatcgtattctgaagttttaatcttactatagaatcattggtgttttcatttcattttgaaaaggtaattgttcttacatattcagGGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTCCGTACTGGAGCATATGACCACACTGGCAAGACATTTTCGACTGCAGAGG

Basic information

species Zea mays
transcript GRMZM2G157034_T01
intron # 9
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|33094592|gb|CF054586.1|CF054586
EST:     TAATCAAAGTATGGGAAACTTCTCAGGGAAAGTTGGTCAAAACATTGAAG                         GGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTC
genomic: TAATCAAAGTATGGGAAACTTCTCAGGGAAAGTTGGTCAAAACATTGAAGgtatgcatca ... acatattcagGGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTC
EST: gi|211305746|gb|FK970549.1|FK970549
EST:     TAATCAAAGTATGGGAAACTTCTCAGGGAAAGTTGGTCAAAACATTGAAG                         GGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTC
genomic: TAATCAAAGTATGGGAAACTTCTCAGGGAAAGTTGGTCAAAACATTGAAGgtatgcatca ... acatattcagGGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTC
EST: gi|50328574|gb|CO523700.1|CO523700
EST:     TAATCAAAGTATGGGAAACTTCTCAGGGAAAGTTGGTCAAAACATTGAAG                         GGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTC
genomic: TAATCAAAGTATGGGAAACTTCTCAGGGAAAGTTGGTCAAAACATTGAAGgtatgcatca ... acatattcagGGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTC
EST: gi|211305745|gb|FK970548.1|FK970548
EST:     CAAAACATTGAAG                         GGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTC
genomic: CAAAACATTGAAGgtatgcatca ... acatattcagGGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTC
EST: gi|32939016|gb|CF043835.1|CF043835
EST:     TAATCAAAGTATGGGAAACTTCTCAGGGAAAGTTGGTCAAAACATTGAAG                         GGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTC
genomic: TAATCAAAGTATGGGAAACTTCTCAGGGAAAGTTGGTCAAAACATTGAAGgtatgcatca ... acatattcagGGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTC
EST: gi|32930416|gb|CF035228.1|CF035228
EST:     TAATCAAAGTATGGGAAACTTCTCAGGGAAAGTTGGTCAAAACATTGAAG                         GGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTC
genomic: TAATCAAAGTATGGGAAACTTCTCAGGGAAAGTTGGTCAAAACATTGAAGgtatgcatca ... acatattcagGGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatcattggtgttttcatttcattttgaaaaggtaattgttcttacatattcagGGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTCCGTACTGGAGCATATGACCACACTGGCAAGACATTTTCGACTGCAGAGG
                                        ttcttac  putative branch site (score: 2)
                                        ttcttac  CT-rich tract
            ttttcatttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgtagtttacttaatcgtattctgaagttttaatcttactatagaatcattggtgttttcatttcattttgaaaaggtaattgttcttacatattcagGGTCATGGGCACTGGGTGAATTCGCTTGCTTTGAGCACGGAATATGTTCTCCGTACTGGAGCATATGACCACACTGGCAAGACATTTTCGACTGCAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG