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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacacatcctgcttatccagctgttatttgaatcttatatcttgccattgactggttatgtggccatgagacacttttactaaatcataccaactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAG

Basic information

species Zea mays
transcript GRMZM2G030902_T03
intron # 1
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|211330813|gb|FL315989.1|FL315989
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAG
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAG
EST: gi|211099331|gb|FL362931.1|FL362931
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAG
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAG

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: 290

GGGCGAGCGCCGCCTCCCCTCCCTCGCTCCGTGAGGTCCTCGCCGGCGACGAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 157

GGGCGAGCGCCGCCTCCCCTCCCTCGCTCCGTGAGGTCCTCGCCGGCGACGAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 76

GGGCGAGCGCCGCCTCCCCTCCCTCGCTCCGTGAGGTCCTCGCCGGCGACGAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 214

GGGCGAGCGCCGCCTCCCCTCCCTCGCTCCGTGAGGTCCTCGCCGGCGACGAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgactggttatgtggccatgagacacttttactaaatcataccaactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAG
                                tactaaa  putative branch site (score: 214)
                                                ctttc  putative PPT
                             ttttactaaatcata  TA-rich tract