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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaagtattgtcattgtccttgttttatgtgtctgctatcttttctgatgtttcctttccctgaataaactaatttattctgttgctatcaccatatggcagGCTATGAGTGAGAAGGAAGCATTTGAGATGAAAGCTGAACTAGAGACCAAGGGGGAGACAAATTTTAAAGTCTGCACACTTGGAAAAGACGTGGTGATTA

Basic information

species Zea mays
transcript GRMZM5G821551_T02
intron # 7
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|32850719|gb|CD990400.1|CD990400
EST:     TGGGGCTGGCTTTTAAGGGCAACCAAAAGATGGCCCTGGAAGCATTGGAG                         GCTATGAGTGAGAAGGAAGCATTTGAGATGAAAGCTGAACTAGAGACCAAG
genomic: TGGGGCTGGCTTTTAAGGGCAACCAAAAGATGGTCCTGGAAGCATTGGAGgtaacaagta ... catatggcagGCTATGAGTGAGAAGGAAGCATTTGAGATGAAAGCTGAACTAGAGACCAAG
EST: gi|31349469|gb|CD433826.1|CD433826
EST:     TGGGGCTGGCTTTTAAGGGCAACCAAAAGATGGTCCTGGAAGCATTGGAG                         GCTATGAGTGAGAAGGAAGCATTTGAGATGAAAGCTGAACTAGAGACCAAG
genomic: TGGGGCTGGCTTTTAAGGGCAACCAAAAGATGGTCCTGGAAGCATTGGAGgtaacaagta ... catatggcagGCTATGAGTGAGAAGGAAGCATTTGAGATGAAAGCTGAACTAGAGACCAAG
EST: gi|31349068|gb|CD433425.1|CD433425
EST:     TGGGGCTGGCTTTTAAGGGCAACCAAAAGATGGTCCTGGAAGCATTGGAG                         GCTATGAGTGAGAAGGAAGCATTTGAGATGAAAGCTGAACTAGAGACCAAG
genomic: TGGGGCTGGCTTTTAAGGGCAACCAAAAGATGGTCCTGGAAGCATTGGAGgtaacaagta ... catatggcagGCTATGAGTGAGAAGGAAGCATTTGAGATGAAAGCTGAACTAGAGACCAAG

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: 45 (upstream exon), 48 (downstream exon)
Score: 164

AAACTTGTCATAGTTCCCTCGAAGAAAGACCTGGGGCTGGCTTTTAAGGGCAACCAAAAGATGGTCCTGGAAGCATTGGAGgtaacaagta ... catatggcagGCTATGAGTGAGAAGGAAGCATTTGAGATGAAAGCTGAACTAGAGACCAAGGGGGAGACAAATTTTAAAGTCTGCACACTTGGAAAAGACGTGGTGATTA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 85

AAACTTGTCATAGTTCCCTCGAAGAAAGACCTGGGGCTGGCTTTTAAGGGCAACCAAAAGATGGTCCTGGAAGCATTGGAGgtaacaagta ... catatggcagGCTATGAGTGAGAAGGAAGCATTTGAGATGAAAGCTGAACTAGAGACCAAGGGGGAGACAAATTTTAAAGTCTGCACACTTGGAAAAGACGTGGTGATTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 139

AAACTTGTCATAGTTCCCTCGAAGAAAGACCTGGGGCTGGCTTTTAAGGGCAACCAAAAGATGGTCCTGGAAGCATTGGAGgtaacaagta ... catatggcagGCTATGAGTGAGAAGGAAGCATTTGAGATGAAAGCTGAACTAGAGACCAAGGGGGAGACAAATTTTAAAGTCTGCACACTTGGAAAAGACGTGGTGATTA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 114

AAACTTGTCATAGTTCCCTCGAAGAAAGACCTGGGGCTGGCTTTTAAGGGCAACCAAAAGATGGTCCTGGAAGCATTGGAGgtaacaagta ... catatggcagGCTATGAGTGAGAAGGAAGCATTTGAGATGAAAGCTGAACTAGAGACCAAGGGGGAGACAAATTTTAAAGTCTGCACACTTGGAAAAGACGTGGTGATTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttcctttccctgaataaactaatttattctgttgctatcaccatatggcagGCTATGAGTGAGAAGGAAGCATTTGAGATGAAAGCTGAACTAGAGACCAAGGGGGAGACAAATTTTAAAGTCTGCACACTTGGAAAAGACGTGGTGATTA
                    aactaat  putative branch site (score: 114)
                aataaactaatttatt  TA-rich tract