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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatccagacctcctggttatggactgggtgatttttgttctgaaatcttatttggttacttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT

Basic information

species Zea mays
transcript GRMZM5G869572_T01
intron # 6
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|211163358|gb|FK967901.1|FK967901
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
EST: gi|31363389|gb|CD447746.1|CD447746
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
EST: gi|89250982|gb|DY622768.1|DY622768
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
EST: gi|6918339|gb|AW399869.1|AW399869
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGACTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
EST: gi|211163359|gb|FK967902.1|FK967902
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
EST: gi|6918594|gb|AW400124.1|AW400124
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGACTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGGCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
EST: gi|60338787|gb|DN205760.1|DN205760
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG

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: 72

GATCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 64

GATCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT


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

GATCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT


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

GATCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttatggactgggtgatttttgttctgaaatcttatttggttacttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT
                                           tacttac  putative branch site (score: 46)
                             aaatcttattt  TA-rich tract