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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAGTTTATAACAGGAGCGATGAAGTTGGTATTGTCCTCTTTGGTACTAAAGgttagttatttatagttgcatcaactgtttctatttgtaccccaaatcgtattgatttatttggtttttggaaactattagctgagccttttttttcttg...

Basic information

species Zea mays
transcript GRMZM2G137968_T02
intron # 3
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|22489351|gb|BU049274.1|BU049274
EST:     TTGGTACTAAAG                         GAACATGCAATGAGCTTGCAAAGGACATTGGGGGCTATAAGCATGTGACGG
genomic: TTGGTACTAAAGgttagttatt ... atgtattcagGAACATGCAATGAGCTTGCAAAGGACATTGGGGGCTATAAGCATGTGACGG
EST: gi|71766540|gb|DR964477.1|DR964477
EST:     AGTTTATAACAGGAGCGATGAAGTTGGTATTGTCCTCTTTGGTACTAAAG                         GAACATGCAATGAGCTTGCAAAGGACATTGGGGGCTATAAGCATGTGACGG
genomic: AGTTTATAACAGGAGCGATGAAGTTGGTATTGTCCTCTTTGGTACTAAAGgttagttatt ... atgtattcagGAACATGCAATGAGCTTGCAAAGGACATTGGGGGCTATAAGCATGTGACGG
EST: gi|18384620|gb|BM417819.1|BM417819
EST:     AGTTTATAACAGGAGCGATGAAGTTGGTATTGTCCTCTTTGGTACTAAAG                         GAACATGCAATGAGCTTGCAAAGGACATTGGGGGCTATAAGCATGTGACGG
genomic: AGTTTATAACAGGAGCGATGAAGTTGGTATTGTCCTCTTTGGTACTAAAGgttagttatt ... atgtattcagGAACATGCAATGAGCTTGCAAAGGACATTGGGGGCTATAAGCATGTGACGG

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: 46 (upstream exon), 49 (downstream exon)
Score: 124

CTAGTTTATAACAGGAGCGATGAAGTTGGTATTGTCCTCTTTGGTACTAAAGgttagttatt ... atgtattcagGAACATGCAATGAGCTTGCAAAGGACATTGGGGGCTATAAGCATGTGACGGTCATACATGATATTAAAGTTGTAGATGAAGGAACGGCACAGGCTCTGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

CTAGTTTATAACAGGAGCGATGAAGTTGGTATTGTCCTCTTTGGTACTAAAGgttagttatt ... atgtattcagGAACATGCAATGAGCTTGCAAAGGACATTGGGGGCTATAAGCATGTGACGGTCATACATGATATTAAAGTTGTAGATGAAGGAACGGCACAGGCTCTGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

CTAGTTTATAACAGGAGCGATGAAGTTGGTATTGTCCTCTTTGGTACTAAAGgttagttatt ... atgtattcagGAACATGCAATGAGCTTGCAAAGGACATTGGGGGCTATAAGCATGTGACGGTCATACATGATATTAAAGTTGTAGATGAAGGAACGGCACAGGCTCTGCA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 22

CTAGTTTATAACAGGAGCGATGAAGTTGGTATTGTCCTCTTTGGTACTAAAGgttagttatt ... atgtattcagGAACATGCAATGAGCTTGCAAAGGACATTGGGGGCTATAAGCATGTGACGGTCATACATGATATTAAAGTTGTAGATGAAGGAACGGCACAGGCTCTGCA