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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttgcctaccatgtccctgcgtcctggagatgtcaagtcgtcaacggagatttgatctgacaaatgcttcctgcacttggcgccaacatttgttttttgtgtggctgcaactgtgaacccatttaacttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA

Basic information

species Zea mays
transcript GRMZM2G009021_T01
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|37396358|gb|CF635468.1|CF635468
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|30087497|gb|CB885703.1|CB885703
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|29945970|gb|CB815912.1|CB815912
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211502290|gb|FL183062.1|FL183062
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATATTCCTGATGACACTGTATTGACCTGCTCACGTGGC
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT

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: 112

GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 47

GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 40

GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 81

GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccaacatttgttttttgtgtggctgcaactgtgaacccatttaacttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA
                                           aacttac  putative branch site (score: 81)
      atttgtttttt  TA-rich tract