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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtggttgttagccattttcttcaaaactgccttgaatttcttttttaacatattttatatacactctatgttcttaaacatatgccattcatcagGACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGGCAAAAGGCAAATATTGATGCAGCGGTCAGAAAG

Basic information

species Zea mays
transcript GRMZM2G119725_T04
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|211138740|gb|FL068273.1|FL068273
EST:     TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAG                         GACCTTACTAGCGAGCCGAAGTATCTTGTTACTTTTACTGGTGGGGATGGG
genomic: TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggtt ... cattcatcagGACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGT-ATTGG
EST: gi|211445045|gb|FL132441.1|FL132441
EST:     TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAG                         GACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGG
genomic: TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggtt ... cattcatcagGACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGG

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), 46 (downstream exon)
Score: 190

TGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggtt ... cattcatcagGACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGGCAAAAGGCAAATATTGATGCAGCGGTCAGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

TGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggtt ... cattcatcagGACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGGCAAAAGGCAAATATTGATGCAGCGGTCAGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

TGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggtt ... cattcatcagGACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGGCAAAAGGCAAATATTGATGCAGCGGTCAGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

TGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggtt ... cattcatcagGACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGGCAAAAGGCAAATATTGATGCAGCGGTCAGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttaacatattttatatacactctatgttcttaaacatatgccattcatcagGACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGGCAAAAGGCAAATATTGATGCAGCGGTCAGAAAG
  ttttaac  putative branch site (score: 180)
     taacatattttatata  TA-rich tract