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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttccttttcatcttgagttatagacataccctaaggcagaatatttaagtctaatgatatttacattcccttttagCAATATGGAGACATGCAGACACTTAATGCTTCTTGCAAACATCATGGTTTTGTGATGGTATCTTACTATGATATAAGATCGGCAGAAAATGCTATGAGGG

Basic information

species Zea mays
transcript GRMZM2G451716_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|32945350|gb|CF050169.1|CF050169
EST:     GAAACATTGATAGCAACGTCGAGGATTCTGAATTGAAATTCATGTTTGAG                         CAATATGGAGACATGCAGACACTTAATGCTTCTTGCAAACATCATGGTTTT
genomic: GAAACATTGATAGCAACGTCGAGGATTCTGAATTGAAATTCATGTTTGAGgtaagttttc ... tcccttttagCAATATGGAGACATGCAGACACTTAATGCTTCTTGCAAACATCATGGTTTT




















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: 313

GTCAATTGTCCAACTCAATGGTGAGCGATCCTCGAGAATCCTTTTTGTCGGAAACATTGATAGCAACGTCGAGGATTCTGAATTGAAATTCATGTTTGAGgtaagttttc ... tcccttttagCAATATGGAGACATGCAGACACTTAATGCTTCTTGCAAACATCATGGTTTTGTGATGGTATCTTACTATGATATAAGATCGGCAGAAAATGCTATGAGGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 169

GTCAATTGTCCAACTCAATGGTGAGCGATCCTCGAGAATCCTTTTTGTCGGAAACATTGATAGCAACGTCGAGGATTCTGAATTGAAATTCATGTTTGAGgtaagttttc ... tcccttttagCAATATGGAGACATGCAGACACTTAATGCTTCTTGCAAACATCATGGTTTTGTGATGGTATCTTACTATGATATAAGATCGGCAGAAAATGCTATGAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

GTCAATTGTCCAACTCAATGGTGAGCGATCCTCGAGAATCCTTTTTGTCGGAAACATTGATAGCAACGTCGAGGATTCTGAATTGAAATTCATGTTTGAGgtaagttttc ... tcccttttagCAATATGGAGACATGCAGACACTTAATGCTTCTTGCAAACATCATGGTTTTGTGATGGTATCTTACTATGATATAAGATCGGCAGAAAATGCTATGAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

GTCAATTGTCCAACTCAATGGTGAGCGATCCTCGAGAATCCTTTTTGTCGGAAACATTGATAGCAACGTCGAGGATTCTGAATTGAAATTCATGTTTGAGgtaagttttc ... tcccttttagCAATATGGAGACATGCAGACACTTAATGCTTCTTGCAAACATCATGGTTTTGTGATGGTATCTTACTATGATATAAGATCGGCAGAAAATGCTATGAGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacataccctaaggcagaatatttaagtctaatgatatttacattcccttttagCAATATGGAGACATGCAGACACTTAATGCTTCTTGCAAACATCATGGTTTTGTGATGGTATCTTACTATGATATAAGATCGGCAGAAAATGCTATGAGGG
                           gtctaat  putative branch site (score: 113)
                                      tttacattccctttt  putative PPT
                  aatatttaagtctaat  TA-rich tract