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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcattctatgtctttgtcctcatattttattactagattcttgttatcatttcttatttattagtacttaatttattttgcttataatgattcagCCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAG

Basic information

species Zea mays
transcript GRMZM2G344924_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|78091213|gb|DV519587.1|DV519587
EST:     CTAATCCGGGCAGTCTGTTTAGCAGCAGCGGTCCTTCACTTTTTTCCACA                         CCAACTTTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCT
genomic: CTAATCCGGGCAGTCTGTTTAGCAGCAGCGGTCCTTCACTTTTTTCAACAgtaagcattc ... aatgattcagCCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCT
EST: gi|31358918|gb|CD443275.1|CD443275
EST:     CTAATCCGGGCAGTCTGTTTAGCAGCAGCGGTCCTTCACTTTTTTCAACA                         CCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTC
genomic: CTAATCCGGGCAGTCTGTTTAGCAGCAGCGGTCCTTCACTTTTTTCAACAgtaagcattc ... aatgattcagCCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTC
EST: gi|20507629|gb|BQ279708.1|BQ279708
EST:     CTAATCCGGGCAGTCTGTTTATTTGCAGCGGTCCTTCACTTTTTTCAACA                         CCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTC
genomic: CTAATCCGGGCAGTCTGTTTAGCAGCAGCGGTCCTTCACTTTTTTCAACAgtaagcattc ... aatgattcagCCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTC
EST: gi|26456661|gb|CA828244.1|CA828244
EST:     CTAATCCGGGCAGTCTGTTTAGCAGCAGCGGTCCTTCACTTTTTTCAACA                         CCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTC
genomic: CTAATCCGGGCAGTCTGTTTAGCAGCAGCGGTCCTTCACTTTTTTCAACAgtaagcattc ... aatgattcagCCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTC

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: 281

ACCGACATCAAGTACACCGGCTTTCTCCTCTGGCAGCCTATTTGGCTCAACTAATCCGGGCAGTCTGTTTAGCAGCAGCGGTCCTTCACTTTTTTCAACAgtaagcattc ... aatgattcagCCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

ACCGACATCAAGTACACCGGCTTTCTCCTCTGGCAGCCTATTTGGCTCAACTAATCCGGGCAGTCTGTTTAGCAGCAGCGGTCCTTCACTTTTTTCAACAgtaagcattc ... aatgattcagCCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

ACCGACATCAAGTACACCGGCTTTCTCCTCTGGCAGCCTATTTGGCTCAACTAATCCGGGCAGTCTGTTTAGCAGCAGCGGTCCTTCACTTTTTTCAACAgtaagcattc ... aatgattcagCCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

ACCGACATCAAGTACACCGGCTTTCTCCTCTGGCAGCCTATTTGGCTCAACTAATCCGGGCAGTCTGTTTAGCAGCAGCGGTCCTTCACTTTTTTCAACAgtaagcattc ... aatgattcagCCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttatcatttcttatttattagtacttaatttattttgcttataatgattcagCCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAG
                         acttaat  putative branch site (score: 117)
        atttcttatttattag  TA-rich tract