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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcagccactacattgcttactgttcttttttacattttaaagaattcatacaagtctcttagtaacctttttgaacctttttttcctatttgcttgcagCCTCATCTGGTCCTGGGCTTAATATCTCAAATAATCAAG

Basic information

species Zea mays
transcript GRMZM2G081380_T03
intron # 3
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|71313366|gb|DR793232.1|DR793232
EST:     CGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAAGG                         C-TCATCTGGTCCTGGGCTTAATATCTC
genomic: CGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGA-GGgtaaagaatc ... ttgcttgcagCCTCATCTGGTCCTGGGCTTAATATCTC
EST: gi|148970201|gb|EE021132.2|EE021132
EST:     TCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGG                         CCTCATCTGGTCCTGGGCTTAATATCTCAAATAATCAAG
genomic: TCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaagaatc ... ttgcttgcagCCTCATCTGGTCCTGGGCTTAATATCTCAAATAATCAAG

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), 49 (downstream exon)
Score: 127

TTGGGAGAAGAACGAGAACCACACGCTTTGCCTCAATTCTGCCAAAGCGATCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaagaatc ... ttgcttgcagCCTCATCTGGTCCTGGGCTTAATATCTCAAATAATCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 58

TTGGGAGAAGAACGAGAACCACACGCTTTGCCTCAATTCTGCCAAAGCGATCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaagaatc ... ttgcttgcagCCTCATCTGGTCCTGGGCTTAATATCTCAAATAATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

TTGGGAGAAGAACGAGAACCACACGCTTTGCCTCAATTCTGCCAAAGCGATCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaagaatc ... ttgcttgcagCCTCATCTGGTCCTGGGCTTAATATCTCAAATAATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129

TTGGGAGAAGAACGAGAACCACACGCTTTGCCTCAATTCTGCCAAAGCGATCGGCTGCACTGTCGTCAACATCGGCACACAAGACCTCGCCGAAGGGAGGgtaaagaatc ... ttgcttgcagCCTCATCTGGTCCTGGGCTTAATATCTCAAATAATCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatacaagtctcttagtaacctttttgaacctttttttcctatttgcttgcagCCTCATCTGGTCCTGGGCTTAATATCTCAAATAATCAAG
               tagtaac  putative branch site (score: 129)
                               cctttttttcctattt  putative PPT
                                 tttttttcctattt  TA-rich tract