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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCATGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCAGCCTCTCATGGTTCACCAACTGGgtaagaagaagagccaaccaaataccccaccaatgcaatccaacagcagcctatctaattaactctaacctactcgtgtgctcttcctcttttatgttcttcag

Basic information

species Zea mays
transcript GRMZM2G127328_T01
intron # 6
splice site 5'
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|211256088|gb|FL474859.1|FL474859
EST:     TCGCAATCTACAAGCCCAAACGGTTCAGCCTCTCATGGTTCACCAACTGG                         ATCTGCATCATCCTTGGAGTGCTTCTGATGGTGCTGGCGCCGATTGGAGGG
genomic: TCGCAATCTACAAGCCCAAACGGTTCAGCCTCTCATGGTTCACCAACTGGgtaagaagaa ... tgttcttcagATCTGCATCATCCTTGGAGTGCTTCTGATGGTGCTGGCGCCGATTGGAGGG
EST: gi|32840329|gb|CD980010.1|CD980010
EST:     CCTCTCATGGTTCACCAACTGG                         ATCTGCATCATCCTTGGAGTGCTTCTGATGGTGCTGGCGCCGATTGGAGGG
genomic: CCTCTCATGGTTCACCAACTGGgtaagaagaa ... tgttcttcagATCTGCATCATCCTTGGAGTGCTTCTGATGGTGCTGGCGCCGATTGGAGGG
EST: gi|24934362|gb|CA452580.1|CA452580
EST:     TCGCAATCTACAAGCCCAAACGGTTCAGCCTCTCATGGTTCACCAACTGG                         ATCTGCATCATCCTTGGAGTGCTTCTGATGGTTTTGGCGCCGATTGGAGGG
genomic: TCGCAATCTACAAGCCCAAACGGTTCAGCCTCTCATGGTTCACCAACTGGgtaagaagaa ... tgttcttcagATCTGCATCATCCTTGGAGTGCTTCTGATGGTGCTGGCGCCGATTGGAGGG
EST: gi|32840328|gb|CD980009.1|CD980009
EST:     CGCAATCTACAAGCCCAAACGGTTCAGGCCTCTCATGGTTCACCAACTGG                         ATCTGCATCATCCTTGGAGTGCTTCTGATGGTGCTGGCGCCGATTGGAGGG
genomic: CGCAATCTACAAGCCCAAACGGTTCA-GCCTCTCATGGTTCACCAACTGGgtaagaagaa ... tgttcttcagATCTGCATCATCCTTGGAGTGCTTCTGATGGTGCTGGCGCCGATTGGAGGG

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 2 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 105

CTTCCATGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCAGCCTCTCATGGTTCACCAACTGGgtaagaagaa ... tgttcttcagATCTGCATCATCCTTGGAGTGCTTCTGATGGTGCTGGCGCCGATTGGAGGGCTCCGGCAGATCATTATCAGCGCCAAGACATACAAGTTCTACCAGTAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

CTTCCATGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCAGCCTCTCATGGTTCACCAACTGGgtaagaagaa ... tgttcttcagATCTGCATCATCCTTGGAGTGCTTCTGATGGTGCTGGCGCCGATTGGAGGGCTCCGGCAGATCATTATCAGCGCCAAGACATACAAGTTCTACCAGTAAA




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