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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactattgtttgacaaaaaaatgtgatatatattccacttgcagttatctagatctgacagttatcttgaatttccagTAATTCTATACCACTCTGTTTTCCACTACAAATGTCGTCCCGAGAAAGGCTACATCCGTGCATGTCTTAAAA

Basic information

species Zea mays
transcript GRMZM2G069976_T01
intron # 11
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|32834610|gb|CD974288.1|CD974288
EST:     AGATCTATTACTTAGACGATATTGGAGGCGAGAAGATGATGGAACTTATG                         TAATTCTATACCACTCTGTTTTCCACCACAAATGTCGTCCCGAGAAAGGCT
genomic: AGATCTATTACTTAGACGATATTGGAGGCGAGAAGATGATGGAACTTATGgtactattgt ... gaatttccagTAATTCTATACCACTCTGTTTTCCACTACAAATGTCGTCCCGAGAAAGGCT




















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: 179

GGGAATGAGAAAGAGAGATCTATTACTTAGACGATATTGGAGGCGAGAAGATGATGGAACTTATGgtactattgt ... gaatttccagTAATTCTATACCACTCTGTTTTCCACTACAAATGTCGTCCCGAGAAAGGCTACATCCGTGCATGTCTTAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

GGGAATGAGAAAGAGAGATCTATTACTTAGACGATATTGGAGGCGAGAAGATGATGGAACTTATGgtactattgt ... gaatttccagTAATTCTATACCACTCTGTTTTCCACTACAAATGTCGTCCCGAGAAAGGCTACATCCGTGCATGTCTTAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 230

GGGAATGAGAAAGAGAGATCTATTACTTAGACGATATTGGAGGCGAGAAGATGATGGAACTTATGgtactattgt ... gaatttccagTAATTCTATACCACTCTGTTTTCCACTACAAATGTCGTCCCGAGAAAGGCTACATCCGTGCATGTCTTAAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 163

GGGAATGAGAAAGAGAGATCTATTACTTAGACGATATTGGAGGCGAGAAGATGATGGAACTTATGgtactattgt ... gaatttccagTAATTCTATACCACTCTGTTTTCCACTACAAATGTCGTCCCGAGAAAGGCTACATCCGTGCATGTCTTAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatatatattccacttgcagttatctagatctgacagttatcttgaatttccagTAATTCTATACCACTCTGTTTTCCACTACAAATGTCGTCCCGAGAAAGGCTACATCCGTGCATGTCTTAAAA
                             atctgac  putative branch site (score: 163)
                                                tttcc  putative PPT
                                           ttgaattt  TA-rich tract