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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagcatactgtttttcaaatgcattggggtagggaatcctgtgctctctattttagggtatgaatatatgaatgaatactaagcaaacaattatatttagGTGCGGAACAAGTAAATGAAAAACAAAACAGAAAAAGAAAAGGAGTCAGTACAAACCTGACCAGCAGGAAAGCACAACGTG

Basic information

species Zea mays
transcript GRMZM2G067067_T09
intron # 1
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|211050119|gb|FL008128.1|FL008128
EST:     GAGGCGCGCCTCGAAGAAATCCTTGTCGTCTGCCGCGACCGCTAGCGCTG                         GTGCGGATCTAGTCAATGAAAAACA
genomic: GAGGCGCGCCTCGAAGAAATCCTTGTCGTCTGCCGCGACCGCTAGCGCTGgtaccgcccc ... ttatatttagGTGCGGAACAAGTAAATGAAAAACA
EST: gi|211050120|gb|FL008129.1|FL008129
EST:     GAGGCGCGCCTCGAAGAAATCCTTGTCGTCTGCCGCGACCGCTAGCGCTG                         GTGCGGAACAAGTAAAT
genomic: GAGGCGCGCCTCGAAGAAATCCTTGTCGTCTGCCGCGACCGCTAGCGCTGgtaccgcccc ... ttatatttagGTGCGGAACAAGTAAAT
EST: gi|211050121|gb|FL008130.1|FL008130
EST:     GAGGCGCGCCTCGAAGAAATCCTTGTCGTCTGCCGCGACCGCTAGCGCTG                         GTGCGGAACAAGTAAATG
genomic: GAGGCGCGCCTCGAAGAAATCCTTGTCGTCTGCCGCGACCGCTAGCGCTGgtaccgcccc ... ttatatttagGTGCGGAACAAGTAAATG

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: 39 (upstream exon), 47 (downstream exon)
Score: 6

CAGACGCGGAAGAGGGTGGGTTCAGGAGCAAGCCAGCCTGCCGCCACCATGAGGCGCGCCTCGAAGAAATCCTTGTCGTCTGCCGCGACCGCTAGCGCTGgtaccgcccc ... ttatatttagGTGCGGAACAAGTAAATGAAAAACAAAACAGAAAAAGAAAAGGAGTCAGTACAAACCTGACCAGCAGGAAAGCACAACGTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 11

CAGACGCGGAAGAGGGTGGGTTCAGGAGCAAGCCAGCCTGCCGCCACCATGAGGCGCGCCTCGAAGAAATCCTTGTCGTCTGCCGCGACCGCTAGCGCTGgtaccgcccc ... ttatatttagGTGCGGAACAAGTAAATGAAAAACAAAACAGAAAAAGAAAAGGAGTCAGTACAAACCTGACCAGCAGGAAAGCACAACGTG


Block sizes: 30 (upstream exon), 46 (downstream exon)
Score: 17

CAGACGCGGAAGAGGGTGGGTTCAGGAGCAAGCCAGCCTGCCGCCACCATGAGGCGCGCCTCGAAGAAATCCTTGTCGTCTGCCGCGACCGCTAGCGCTGgtaccgcccc ... ttatatttagGTGCGGAACAAGTAAATGAAAAACAAAACAGAAAAAGAAAAGGAGTCAGTACAAACCTGACCAGCAGGAAAGCACAACGTG


Block sizes: 28 (upstream exon), 46 (downstream exon)
Score: 2

CAGACGCGGAAGAGGGTGGGTTCAGGAGCAAGCCAGCCTGCCGCCACCATGAGGCGCGCCTCGAAGAAATCCTTGTCGTCTGCCGCGACCGCTAGCGCTGgtaccgcccc ... ttatatttagGTGCGGAACAAGTAAATGAAAAACAAAACAGAAAAAGAAAAGGAGTCAGTACAAACCTGACCAGCAGGAAAGCACAACGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctattttagggtatgaatatatgaatgaatactaagcaaacaattatatttagGTGCGGAACAAGTAAATGAAAAACAAAACAGAAAAAGAAAAGGAGTCAGTACAAACCTGACCAGCAGGAAAGCACAACGTG
                                       aaacaattatattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagcatactgtttttcaaatgcattggggtagggaatcctgtgctctctattttagggtatgaatatatgaatgaatactaagcaaacaattatatttagGTGCGGAACAAGTAAATGAAAAACAAAACAGAAAAAGAAAAGGAGTCAGTACAAACCTGACCAGCAGGAAAGCACAACGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG