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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtaggtttatatttaaacctctctgtttttttacaatttatcttcaaacactaatttgggcttaacttatgttcaaatgcatgcatgcatggatacatcagCTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCC

Basic information

species Zea mays
transcript GRMZM2G344924_T01
intron # 6
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|31358918|gb|CD443275.1|CD443275
EST:     CCCTGCTCAAACTTCGAACTTATTCTCCTTCCGACCTCCAATTCAACCAG                         CTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGA
genomic: CCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAGgtcagtaggt ... gatacatcagCTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGA
EST: gi|20507629|gb|BQ279708.1|BQ279708
EST:     CCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAG                         CTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGA
genomic: CCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAGgtcagtaggt ... gatacatcagCTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGA
EST: gi|78116408|gb|DV534795.1|DV534795
EST:     CTCCTTCCAACCTCCAATTCAACCAG                         CTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGA
genomic: CTCCTTCCAACCTCCAATTCAACCAGgtcagtaggt ... gatacatcagCTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGA
EST: gi|26456661|gb|CA828244.1|CA828244
EST:     CCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAG                         CTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGA
genomic: CCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAGgtcagtaggt ... gatacatcagCTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGA

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), 48 (downstream exon)
Score: 270

CCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAGgtcagtaggt ... gatacatcagCTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 114

CCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAGgtcagtaggt ... gatacatcagCTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 100

CCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAGgtcagtaggt ... gatacatcagCTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

CCAACATTTCAACCATCGGCCCCTGCTCAAACTTCGAACTTATTCTCCTTCCAACCTCCAATTCAACCAGgtcagtaggt ... gatacatcagCTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacactaatttgggcttaacttatgttcaaatgcatgcatgcatggatacatcagCTTCTACAGGTGGATTCCCTGGTTTTTCCAATACTACAAACCAAGCCTTGATGGGACAGCC
               ttaacttat  TA-rich tract