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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagctatttctaatttatgcagaattctagaatgttggaatgacttatcatttggcatggagttcataaaaatgattgatgtttccattttcaactagAGATGGTGGTGAAGTCTCAACACGGGATCTGCAGAAAATCGTTCAAGCATTACCCCAATACAGTGATCAAGTTGAGAAATTGACGCTACATATAGAG

Basic information

species Zea mays
transcript GRMZM5G830776_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G830776_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g04450.2 (Oryza sativa), 3'ss of exon 12
ttgagctatttctaatttatgcagaattctag--aatgttggaatgacttatcatttggcatggagttcataa-aaatgattgatgtttccattttcaactagAGATGGTGGTGAAGTCTCAACACGGGATCTGCAGAAAATCGTTCAAGCATTACCCCAATACAGTGATCAAGTTGAGAAATTGACGCTACATATAGAG
| | | || | | | | | | |||| || || | || || | |||||| ||| || || || || |||| |||||||||||||||| | || ||| |||||||||||| ||||||||||| || || |||||| |||| ||||||||||||||||| || |||||||||
-tcaaatgttgatcgatca-gttgtttgctagccaaagtacagaaagtgcattgttctaagttct-ttcatattgcatgcttatgattccctttctcaattagAGATGGTGGTGAAATTTCTACAAAGGATCTGCAGAAGATCGTTCAAGCTTTGCCACAATACGGTGAACAAGTTGAGAAATTGACCCTCCATATAGAG
















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: 41 (upstream exon), 48 (downstream exon)
Score: 8

GCTAGTGAGAGGTTGTACGAAAAGATGAACAATTTTGTTGCCAAGAATAAAGCAGCACAACTTTCAAGgtgcctaacc ... tttcaactagAGATGGTGGTGAAGTCTCAACACGGGATCTGCAGAAAATCGTTCAAGCATTACCCCAATACAGTGATCAAGTTGAGAAATTGACGCTACATATAGAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 29

GCTAGTGAGAGGTTGTACGAAAAGATGAACAATTTTGTTGCCAAGAATAAAGCAGCACAACTTTCAAGgtgcctaacc ... tttcaactagAGATGGTGGTGAAGTCTCAACACGGGATCTGCAGAAAATCGTTCAAGCATTACCCCAATACAGTGATCAAGTTGAGAAATTGACGCTACATATAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

GCTAGTGAGAGGTTGTACGAAAAGATGAACAATTTTGTTGCCAAGAATAAAGCAGCACAACTTTCAAGgtgcctaacc ... tttcaactagAGATGGTGGTGAAGTCTCAACACGGGATCTGCAGAAAATCGTTCAAGCATTACCCCAATACAGTGATCAAGTTGAGAAATTGACGCTACATATAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

GCTAGTGAGAGGTTGTACGAAAAGATGAACAATTTTGTTGCCAAGAATAAAGCAGCACAACTTTCAAGgtgcctaacc ... tttcaactagAGATGGTGGTGAAGTCTCAACACGGGATCTGCAGAAAATCGTTCAAGCATTACCCCAATACAGTGATCAAGTTGAGAAATTGACGCTACATATAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatcatttggcatggagttcataaaaatgattgatgtttccattttcaactagAGATGGTGGTGAAGTCTCAACACGGGATCTGCAGAAAATCGTTCAAGCATTACCCCAATACAGTGATCAAGTTGAGAAATTGACGCTACATATAGAG
                              gattgat  putative branch site (score: 53)
 tttccattttc  CT-rich tract
 ttcataaaaatgatt  TA-rich tract