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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgtttctcctgatgcacaatatctttgttttgcagaaaaatactatcttctttactgaacatgtggtccaaattgtaccagATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAATTTCTTCAGTTGAAACTGATGTTAACCAACTTCCCCTTATGGTTTCTGA

Basic information

species Zea mays
transcript GRMZM2G332809_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|32914633|gb|CF019445.1|CF019445
EST:     CCAGATGAATAAGCTTCTGTCCAAGCATATACGTCCTCTGGAGAGTAAAA                         ATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAA
genomic: CCAGATGAATAAGCTTCTGTCCAAGCATATACGTCCTCTGGAGAGTAAAAgtaggtgttt ... attgtaccagATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAA
EST: gi|29130777|gb|CB381481.1|CB381481
EST:     CCAGATGAATAAGCTTCTGTCCAAGCATATACGTCCTCTGGAGAGTAAAA                         ATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAA
genomic: CCAGATGAATAAGCTTCTGTCCAAGCATATACGTCCTCTGGAGAGTAAAAgtaggtgttt ... attgtaccagATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAA
EST: gi|29945156|gb|CB815497.1|CB815497
EST:     CCAGATGAATAAGCTTCTGTCCAAGCATATACGTCCTCTGGAGAGTAAAA                         ATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAA
genomic: CCAGATGAATAAGCTTCTGTCCAAGCATATACGTCCTCTGGAGAGTAAAAgtaggtgttt ... attgtaccagATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAA
EST: gi|9028641|gb|BE238681.1|BE238681
EST:     CCAGATGAATAAGCTTCTGTCCAAGCATATACGTCCTCTGGAGAGTAAAA                         ATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAA
genomic: CCAGATGAATAAGCTTCTGTCCAAGCATATACGTCCTCTGGAGAGTAAAAgtaggtgttt ... attgtaccagATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAA

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: 250

TGCAATGATGAGCTCCGATTAGTTTTTGAGACTGATAGCACGGACATGTTCCAGATGAATAAGCTTCTGTCCAAGCATATACGTCCTCTGGAGAGTAAAAgtaggtgttt ... attgtaccagATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAATTTCTTCAGTTGAAACTGATGTTAACCAACTTCCCCTTATGGTTTCTGA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 99

TGCAATGATGAGCTCCGATTAGTTTTTGAGACTGATAGCACGGACATGTTCCAGATGAATAAGCTTCTGTCCAAGCATATACGTCCTCTGGAGAGTAAAAgtaggtgttt ... attgtaccagATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAATTTCTTCAGTTGAAACTGATGTTAACCAACTTCCCCTTATGGTTTCTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 123

TGCAATGATGAGCTCCGATTAGTTTTTGAGACTGATAGCACGGACATGTTCCAGATGAATAAGCTTCTGTCCAAGCATATACGTCCTCTGGAGAGTAAAAgtaggtgttt ... attgtaccagATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAATTTCTTCAGTTGAAACTGATGTTAACCAACTTCCCCTTATGGTTTCTGA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 64

TGCAATGATGAGCTCCGATTAGTTTTTGAGACTGATAGCACGGACATGTTCCAGATGAATAAGCTTCTGTCCAAGCATATACGTCCTCTGGAGAGTAAAAgtaggtgttt ... attgtaccagATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAATTTCTTCAGTTGAAACTGATGTTAACCAACTTCCCCTTATGGTTTCTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgcagaaaaatactatcttctttactgaacatgtggtccaaattgtaccagATGATTCGAAACCAGAAGCAAAGAAATTGAAGCCACAGGGTGATGAACCAATTTCTTCAGTTGAAACTGATGTTAACCAACTTCCCCTTATGGTTTCTGA
         aaaaatactatctt  TA-rich tract