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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaccttgtgtgatagtcactgtaaaaaactattctttacatgtagtatctttctagtctttactattttcaatgtattttttatagGTGAAGAATTCTTTACCCGAGGGCTTAGCTAAGGATGATTGGTGCTGGGACCAGAGTATCTTGAATATAGATGTTGGTACTGATGATGTGAGAGACATTG

Basic information

species Zea mays
transcript GRMZM2G014788_T01
intron # 16
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|31361460|gb|CD445817.1|CD445817
EST:     ATGTTAATTTTGTGTTTAAGAAAGTATTTCCTGGAAAATATCGTGTAGAG                         GTGAAGAATTCTTTACCCGAGGGCTTAGCTAAGGATGATTGGTGCTGGGAC
genomic: ATGTTAATTTTGTGTTTAAGAAAGTATTTCCTGGAAAATATCGTGTAGAGgtaagacctt ... ttttttatagGTGAAGAATTCTTTACCCGAGGGCTTAGCTAAGGATGATTGGTGCTGGGAC
EST: gi|31359820|gb|CD444177.1|CD444177
EST:     ATGTTAATTTTGTGTTTAAGAAAGTATTTCCTGGAAAATATCGTGTAGAG                         GTGAAGAATTCTTTACCCGAGGGCTTAGCTAAGGATGATTGGTGCTGGGAC
genomic: ATGTTAATTTTGTGTTTAAGAAAGTATTTCCTGGAAAATATCGTGTAGAGgtaagacctt ... ttttttatagGTGAAGAATTCTTTACCCGAGGGCTTAGCTAAGGATGATTGGTGCTGGGAC
EST: gi|78112628|gb|DV531022.1|DV531022
EST:     ATGTTAATTTTGTGTTTAAGAAAGTATTTCCTGGAAAATATCGTGTAGAG                         GTGAAGAATTCTTTACCCGAGGGCTTAGCTAAGGATGATTGGTGCTGGGAC
genomic: ATGTTAATTTTGTGTTTAAGAAAGTATTTCCTGGAAAATATCGTGTAGAGgtaagacctt ... ttttttatagGTGAAGAATTCTTTACCCGAGGGCTTAGCTAAGGATGATTGGTGCTGGGAC

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: 234

GGCTGGCGGAGTTGAACAGGAAAAGAAGACAACTACATTGGAACAAGATAATGTTAATTTTGTGTTTAAGAAAGTATTTCCTGGAAAATATCGTGTAGAGgtaagacctt ... ttttttatagGTGAAGAATTCTTTACCCGAGGGCTTAGCTAAGGATGATTGGTGCTGGGACCAGAGTATCTTGAATATAGATGTTGGTACTGATGATGTGAGAGACATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

GGCTGGCGGAGTTGAACAGGAAAAGAAGACAACTACATTGGAACAAGATAATGTTAATTTTGTGTTTAAGAAAGTATTTCCTGGAAAATATCGTGTAGAGgtaagacctt ... ttttttatagGTGAAGAATTCTTTACCCGAGGGCTTAGCTAAGGATGATTGGTGCTGGGACCAGAGTATCTTGAATATAGATGTTGGTACTGATGATGTGAGAGACATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

GGCTGGCGGAGTTGAACAGGAAAAGAAGACAACTACATTGGAACAAGATAATGTTAATTTTGTGTTTAAGAAAGTATTTCCTGGAAAATATCGTGTAGAGgtaagacctt ... ttttttatagGTGAAGAATTCTTTACCCGAGGGCTTAGCTAAGGATGATTGGTGCTGGGACCAGAGTATCTTGAATATAGATGTTGGTACTGATGATGTGAGAGACATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 187

GGCTGGCGGAGTTGAACAGGAAAAGAAGACAACTACATTGGAACAAGATAATGTTAATTTTGTGTTTAAGAAAGTATTTCCTGGAAAATATCGTGTAGAGgtaagacctt ... ttttttatagGTGAAGAATTCTTTACCCGAGGGCTTAGCTAAGGATGATTGGTGCTGGGACCAGAGTATCTTGAATATAGATGTTGGTACTGATGATGTGAGAGACATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttacatgtagtatctttctagtctttactattttcaatgtattttttatagGTGAAGAATTCTTTACCCGAGGGCTTAGCTAAGGATGATTGGTGCTGGGACCAGAGTATCTTGAATATAGATGTTGGTACTGATGATGTGAGAGACATTG
                                           tatttttt  CT-rich tract
                         tctttactattttcaa  TA-rich tract