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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggccgcaaccggcatccagtcgcttcctgtattttcgccttccttttggaaaccggcgctgcaaagtctgcaactgcaaccgtggctgactctggtctcctctcctcccgaactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCACCTGGGTCGAGAGTGACGCCAAGCTCATCGACAACCCGCAGATGGTTAA

Basic information

species Zea mays
transcript GRMZM2G047143_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047143_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g40940.2 (Oryza sativa), 3'ss of exon 3
gtaagggccgcaaccggcatccagtcgcttcctgtattttcgccttccttttggaaaccggcgctgcaaagtctgcaactgcaaccgtggctgactctggtctcctctcctcccgaactggt----cagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCACCTGGGTCGAGAGTGACGCCAAGCTCATCGACAACCCGCAGATGGTTAA
||||| |||   |||  || |    |   | | || ||      |             |  | |  |||   || | |   || |||     | |  | |  |  |    |     | || |    ||||| | |||||||||||||| ||||| |||| ||||||||  |  ||   ||||||||| ||||| ||||||||||||||||| || || |||||||| ||
gtaagcgccattaccaccacctctacttcttcagtgttcagtgttcatcgcctctgctctcccccccaattcctcccagctcatccgcattcgtcgattgattgattgattgattgattgattttgcagGCATATTCGACGTGCTGGCGTACACCGACATGGACGTCGCGGTGCCCTTCACCTGGGTGGAGAGCGACGCCAAGCTCATCGAGAATCCACAGATGGTGAA
















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|94475185|gb|EB704143.1|EB704143
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTTGACGTGCTGGCCTACACGGACACGGACGTGGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|32800674|gb|CD952910.1|CD952910
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|32797390|gb|CD949626.1|CD949626
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|32790500|gb|CD942736.1|CD942736
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGGGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|32797842|gb|CD950078.1|CD950078
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|32797599|gb|CD949835.1|CD949835
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
EST: gi|94475186|gb|EB704144.1|EB704144
EST:     GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA
genomic: GCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccg ... aactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgcaactgcaaccgtggctgactctggtctcctctcctcccgaactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCACCTGGGTCGAGAGTGACGCCAAGCTCATCGACAACCCGCAGATGGTTAA
                  ggctgac  putative branch site (score: 3)
                              tctcctctcctcccga  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagggccgcaaccggcatccagtcgcttcctgtattttcgccttccttttggaaaccggcgctgcaaagtctgcaactgcaaccgtggctgactctggtctcctctcctcccgaactggtcagGCGTGTTCGACGTGCTGGCCTACACGGACACGGACGTCGACGCTCCGGGCACCTGGGTCGAGAGTGACGCCAAGCTCATCGACAACCCGCAGATGGTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG