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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatcttccttccgtcagagtagtaccgctcggccggtgaacactaatgagaactgtctcgtgacgcagGATGTTATGGATGACATAAATCTCTTCTCGGTGATCACTGTGCTGTCGTTTCTGCTGTCCTGCCCTCTGATGATCTTTGCCGAAGGCATCAAGTTCACCC

Basic information

species Zea mays
transcript GRMZM2G066413_T01
intron # 5
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|211269384|gb|FL189988.1|FL189988
EST:     CCAACCAATCGAGGAACGTCCTCAGCAAGAAACTCCTTGCCGGTGACAAG                         GATGTTATGGATGACATAAATCTCTTCTCGGTGATCACTGTGCTGTCGTTT
genomic: CCAACCAATCGAGGAACGTCCTCAGCAAGAAACTCCTTGCCGGTGACAAGgtgaatcttc ... cgtgacgcagGATGTTATGGATGACATAAATCTCTTCTCGGTGATCACTGTGCTGTCGTTT
EST: gi|67024608|gb|CO453357.1|CO453357
EST:     CCAACCAATCGAGGAACGTCCTCAGCAAGAAACTCCTTGCCGGTGACAAG                         GATGTTATGGATGACATAAATCTCTTCTCGGTGATCACTGTGCTGTCGTTT
genomic: CCAACCAATCGAGGAACGTCCTCAGCAAGAAACTCCTTGCCGGTGACAAGgtgaatcttc ... cgtgacgcagGATGTTATGGATGACATAAATCTCTTCTCGGTGATCACTGTGCTGTCGTTT

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), 23 (downstream exon)
Score: 4

GACCGGGTTTTGGAGCGCCATGGCGTCCAATCTGACCAACCAATCGAGGAACGTCCTCAGCAAGAAACTCCTTGCCGGTGACAAGgtgaatcttc ... cgtgacgcagGATGTTATGGATGACATAAATCTCTTCTCGGTGATCACTGTGCTGTCGTTTCTGCTGTCCTGCCCTCTGATGATCTTTGCCGAAGGCATCAAGTTCACCC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 263

GACCGGGTTTTGGAGCGCCATGGCGTCCAATCTGACCAACCAATCGAGGAACGTCCTCAGCAAGAAACTCCTTGCCGGTGACAAGgtgaatcttc ... cgtgacgcagGATGTTATGGATGACATAAATCTCTTCTCGGTGATCACTGTGCTGTCGTTTCTGCTGTCCTGCCCTCTGATGATCTTTGCCGAAGGCATCAAGTTCACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 404

GACCGGGTTTTGGAGCGCCATGGCGTCCAATCTGACCAACCAATCGAGGAACGTCCTCAGCAAGAAACTCCTTGCCGGTGACAAGgtgaatcttc ... cgtgacgcagGATGTTATGGATGACATAAATCTCTTCTCGGTGATCACTGTGCTGTCGTTTCTGCTGTCCTGCCCTCTGATGATCTTTGCCGAAGGCATCAAGTTCACCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 20

GACCGGGTTTTGGAGCGCCATGGCGTCCAATCTGACCAACCAATCGAGGAACGTCCTCAGCAAGAAACTCCTTGCCGGTGACAAGgtgaatcttc ... cgtgacgcagGATGTTATGGATGACATAAATCTCTTCTCGGTGATCACTGTGCTGTCGTTTCTGCTGTCCTGCCCTCTGATGATCTTTGCCGAAGGCATCAAGTTCACCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagagtagtaccgctcggccggtgaacactaatgagaactgtctcgtgacgcagGATGTTATGGATGACATAAATCTCTTCTCGGTGATCACTGTGCTGTCGTTTCTGCTGTCCTGCCCTCTGATGATCTTTGCCGAAGGCATCAAGTTCACCC
                           cactaat  putative branch site (score: 20)
                                       ctgtctc  putative PPT