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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCCTCCTCATCGGCGACTTTTCCGCCGGCGACAGGAAACAACGAACCAAACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTGgtactgactgcgctggcttaaattgattacgtctatttcttgtatcgttggcaagtaatcctcgccttacttgttcgtgttgttcttccggcag

Basic information

species Zea mays
transcript GRMZM2G053767_T04
intron # 1
splice site 5'
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|211217179|gb|FL271888.1|FL271888
EST:     AACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTG                         TTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATG
genomic: AACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTGgtactgactg ... cttccggcagTTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATG
EST: gi|211245448|gb|FK950836.1|FK950836
EST:     AACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTG                         TTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATG
genomic: AACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTGgtactgactg ... cttccggcagTTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATG
EST: gi|9952730|gb|BE639193.1|BE639193
EST:     AACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTG                         TTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATG
genomic: AACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTGgtactgactg ... cttccggcagTTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATG
EST: gi|211245447|gb|FK950835.1|FK950835
EST:     AACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTG                         TTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATG
genomic: AACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTGgtactgactg ... cttccggcagTTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATG
EST: gi|211245443|gb|FK950831.1|FK950831
EST:     AACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTG                         TTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATG
genomic: AACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTGgtactgactg ... cttccggcagTTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATG
EST: gi|211245442|gb|FK950830.1|FK950830
EST:     AACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTG                         TTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATG
genomic: AACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTGgtactgactg ... cttccggcagTTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

GGGCCTCCTCATCGGCGACTTTTCCGCCGGCGACAGGAAACAACGAACCAAACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTGgtactgactg ... cttccggcagTTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATGAGGAAGCTCAAGTTCCATGAGCAGAAGCTCCTCAAGAGGCACAATTTCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 76

GGGCCTCCTCATCGGCGACTTTTCCGCCGGCGACAGGAAACAACGAACCAAACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTGgtactgactg ... cttccggcagTTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATGAGGAAGCTCAAGTTCCATGAGCAGAAGCTCCTCAAGAGGCACAATTTCT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 77

GGGCCTCCTCATCGGCGACTTTTCCGCCGGCGACAGGAAACAACGAACCAAACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTGgtactgactg ... cttccggcagTTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATGAGGAAGCTCAAGTTCCATGAGCAGAAGCTCCTCAAGAGGCACAATTTCT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 80

GGGCCTCCTCATCGGCGACTTTTCCGCCGGCGACAGGAAACAACGAACCAAACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTGgtactgactg ... cttccggcagTTATTTTTCTTAACCCGGCTTTCTCTCGATTGCTGCGTAAAGTTGAAGATGAGGAAGCTCAAGTTCCATGAGCAGAAGCTCCTCAAGAGGCACAATTTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCCTCCTCATCGGCGACTTTTCCGCCGGCGACAGGAAACAACGAACCAAACCACTTCTCTGTCGAGAGGCGTCGCGCTCCTCTCTTCGCCCTCTGCTGgtactgactgcgctggcttaaattgattacgtctatttcttgtatcgttggcaagtaatcctcgccttacttgttcgtgttgttcttccggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC