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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagctcaaacaacatgactatttctaattttgtgttatttgagcatctattagaaaggtctcactcttttttgtatttatttctgcagGTGACAAATATATTGATGAG

Basic information

species Zea mays
transcript GRMZM2G019361_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019361_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 10
gtcagctcaaacaacat----gactatttctaattttgtgt-tatttgagcatctatta-gaaaggtctcact--cttttttgtatttatttctgcagGTGACAAATATATTGATGAG
|| ||  |||    | |    ||||||||   |  |  ||  ||| |     | | ||  | |  ||   | |    || ||  ||  ||||||||||| ||||||||||||||||||
gttagtacaagttgcctttttgactattttatagctaatgaatatctagagttgtcttgtgcattgttggattgatcttctttaatgaatttctgcagGGGACAAATATATTGATGAG
















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|31361636|gb|CD445993.1|CD445993
EST:     TGTTCAACAAATGGTCAATGAAGCCCTTCAACGGGTGCCTAATGATAATG                         GTGACAAATATATTGATGAG
genomic: TGTTCAACAAATGGTCAATGAAGCCCTTCAACGGGTGCCTAATGATAATGgtcagctcaa ... atttctgcagGTGACAAATATATTGATGAG
EST: gi|91050205|gb|EB160623.1|EB160623
EST:     CAAATGGTCAATGAAGCCCTTCAACGGGTGCCTAATGATAATG                         GTGACAAATATATTGATGAG
genomic: CAAATGGTCAATGAAGCCCTTCAACGGGTGCCTAATGATAATGgtcagctcaa ... atttctgcagGTGACAAATATATTGATGAG

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), 48 (downstream exon)
Score: 155

AAGGAAAATCTGTTCAACAAATGGTCAATGAAGCCCTTCAACGGGTGCCTAATGATAATGgtcagctcaa ... atttctgcagGTGACAAATATATTGATGAG


Block sizes: 49 (upstream exon), 24 (downstream exon)
Score: 89

AAGGAAAATCTGTTCAACAAATGGTCAATGAAGCCCTTCAACGGGTGCCTAATGATAATGgtcagctcaa ... atttctgcagGTGACAAATATATTGATGAG


Block sizes: 47 (upstream exon), 37 (downstream exon)
Score: 95

AAGGAAAATCTGTTCAACAAATGGTCAATGAAGCCCTTCAACGGGTGCCTAATGATAATGgtcagctcaa ... atttctgcagGTGACAAATATATTGATGAG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 72

AAGGAAAATCTGTTCAACAAATGGTCAATGAAGCCCTTCAACGGGTGCCTAATGATAATGgtcagctcaa ... atttctgcagGTGACAAATATATTGATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatttgagcatctattagaaaggtctcactcttttttgtatttatttctgcagGTGACAAATATATTGATGAG
                        gtctcac  putative branch site (score: 72)
                              ctcttttttgtattta  CT-rich tract
                               tcttttttgtatttat  TA-rich tract