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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTAGATCTAGACGTGGACTTCTTCGATAGACCTGAAATGCTTGGCGAGTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgccttcgtgtcagacgggtattttaccccgcaaggaacatgacgagtcctgtcgtttgatgttctttctatcgccag

Basic information

species Zea mays
transcript GRMZM2G147882_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147882_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 5'ss of exon 5
GCTCTAGATCTAGACGTGGACTTCTTCGATAGACCTGAAATGCTTGGCGAGTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgccttcgtgtcagacgggtattttaccccgcaaggaacatgacgagtcctgtcgtttgatgttctttctatcgccag
|||||| | ||||| | ||||||||| |||| ||| ||||||||||||||| ||||||||||  ||||||||||||| || |||||||||||| ||||||||||||| ||| || |   | | |||||||   | |||| ||||| |||| | |||||||||||||||| || | ||  |||
GCTCTAAACCTAGAAGAGGACTTCTTTGATAAACCAGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAGGTGGACAAAAAACAGgtcatgcattcttgccgttcag-tattttattacacaagaaacataacgaattctgtcgtttgatgttccttttttcatcag

upper sequence: GRMZM2G147882_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g09300.3 (Oryza sativa), 5'ss of exon 5
---------------GCTCTAGATCTAGACGTGGACTTCTTCGATAGACCTGAAATGCTTGGCGAGTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgccttcgtgtcagacgggtattttaccccgcaaggaacatgacgagtcctgtcgtttgatgttctttctatcgccag
               |||||| | ||||| | ||||||||| |||| ||| ||||||||||||||| ||||||||||  ||||||||||||| || |||||||||||| ||||||||||||| ||| || |   | | |||||||   | |||| ||||| |||| | |||||||||||||||| || | ||  |||
AGGATTATTGCCCTTGCTCTAAACCTAGAAGAGGACTTCTTTGATAAACCAGAAATGCTTGGCGAGCCCATAGCCACATTAAGGCTCCTGCATTATGAAGgtggacaaaaaacaggtcatgcattcttgccgttcag-tattttattacacaagaaacataacgaattctgtcgtttgatgttccttttttcatcag
















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|32924156|gb|CF028968.1|CF028968
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|32924444|gb|CF029256.1|CF029256
EST:     GTCAATAACCACGCTAAGGCTCCTGCACTACAAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|32858736|gb|CD998417.1|CD998417
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|32923806|gb|CF028618.1|CF028618
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|32924110|gb|CF028922.1|CF028922
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|32923874|gb|CF028686.1|CF028686
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGGAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|32924334|gb|CF029146.1|CF029146
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|32923638|gb|CF028450.1|CF028450
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGAGGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|32923912|gb|CF028724.1|CF028724
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|32923869|gb|CF028681.1|CF028681
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|32923708|gb|CF028520.1|CF028520
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|32924079|gb|CF028891.1|CF028891
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCTAGATCTAGACGTGGACTTCTTCGATAGACCTGAAATGCTTGGCGAGTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgccttcgtgtcagacgggtattttaccccgcaaggaacatgacgagtcctgtcgtttgatgttctttctatcgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA