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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtataatgtagaatgtacagacttataggatattccaaaaatattttatcctgcttttgatttaagcatgtacctgttaaattttgctgtgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGACAGCCACTCTGTGAG

Basic information

species Zea mays
transcript GRMZM2G475017_T03
intron # 2
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|31910491|gb|CD651450.1|CD651450
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCG                         G-TAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCGgtcagcgcca ... tgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
EST: gi|78116119|gb|DV534507.1|DV534507
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCG                         GTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCGgtcagcgcca ... tgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
EST: gi|91876225|gb|EB406182.1|EB406182
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCG                         GTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCGgtcagcgcca ... tgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
EST: gi|94474028|gb|EB702986.1|EB702986
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCG                         GTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCGgtcagcgcca ... tgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
EST: gi|76921023|gb|DV168420.1|DV168420
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCG                         GTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCGgtcagcgcca ... tgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
EST: gi|71775279|gb|DR973157.1|DR973157
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCG                         GTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCGgtcagcgcca ... tgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
EST: gi|38687417|gb|CK144448.1|CK144448
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCG                         GTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCGgtcagcgcca ... tgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
EST: gi|76289471|gb|DV029039.1|DV029039
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCG                         GTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCGgtcagcgcca ... tgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
EST: gi|50338849|gb|CO533975.1|CO533975
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCG                         GTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCGgtcagcgcca ... tgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGA

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: 49 (upstream exon), 47 (downstream exon)
Score: 65

GCGGCCGGGCGAGGCGGACTGCACCTACTACCTCCGCACTGGCGCCTGCGGCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCGgtcagcgcca ... tgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGACAGCCACTCTGTGAG


Block sizes: 35 (upstream exon), 48 (downstream exon)
Score: 28

GCGGCCGGGCGAGGCGGACTGCACCTACTACCTCCGCACTGGCGCCTGCGGCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCGgtcagcgcca ... tgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGACAGCCACTCTGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 29

GCGGCCGGGCGAGGCGGACTGCACCTACTACCTCCGCACTGGCGCCTGCGGCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCGgtcagcgcca ... tgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGACAGCCACTCTGTGAG


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 31

GCGGCCGGGCGAGGCGGACTGCACCTACTACCTCCGCACTGGCGCCTGCGGCTACGGGGAGCGCTGCCGCTACAACCACCCCCGGGATCGGCCGGCTCCGgtcagcgcca ... tgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGACAGCCACTCTGTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatcctgcttttgatttaagcatgtacctgttaaattttgctgtgtttttcagGTTAATGGCGTTGGGAAGACCACAGGTATGGAGTACCCAGAGCGCCCTGGACAGCCACTCTGTGAG
          ttttgat  putative branch site (score: 31)
                                             tgtttttc  putative PPT
          ttttgatttaa  TA-rich tract