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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgatctgcttgttcagggaaaaccattgccatgattatgtctaactttttcctcacttggccacatgattaattttctttatgtgcttttgccattggtaatagGAGGAGACTCAAAAGCATTGATGTTTGTGCAAATTAGCCCATCCGATAATGATGTTTCGGAAACATTGAGTTCACTAAACTTCGCTAGCCGTGTTCGGCG

Basic information

species Zea mays
transcript GRMZM2G092232_T03
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092232_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 5
gtaagatgatctgcttgttcagg-gaaaaccattgccatgatt------------atgtctaacttttt-------------------------------cctcacttggccacatgattaattt--tctttatgtgcttttgc-cattggtaatagGAGGAGACTCAAAAGCATTGATGTTTGTGCAAATTAGCCCATCCGATAATGATGTTTCGGAAACATTGAGTTCACTAAACTTCGCTAGCCGTGTTCGGCG
||||  ||| ||| |  |   |  || ||||||   ||| |||            || || ||  || |                                 |||||| || |||| ||||||||  |||||  |||||| | |  | || |||||||||| ||||||||||| || |||||||||||||||||||||||| | || ||||| || ||||| ||||| ||| | ||||| || || |||||||| ||
gtaacctgacctgttcttctggaagagaaccatcttcataatttatcacttcaatatttccaatcttctatgtattttttgagcaattatcgtgtgtgtctttcacttagctacatcattaatttgctcttttggtgcttcttcatactgataatagGAGGGGACTCAAAAGCTTTAATGTTTGTGCAAATTAGCCCATCCAACAACGATGTGTCAGAAACTTTGAGCTCATTGAACTTTGCAAGTCGTGTTCGTCG
















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: 38 (upstream exon), 48 (downstream exon)
Score: 166

AAATTCTAAATTGACACACTTGCTGCAAGATTCTCTAGgtaagatgat ... ttggtaatagGAGGAGACTCAAAAGCATTGATGTTTGTGCAAATTAGCCCATCCGATAATGATGTTTCGGAAACATTGAGTTCACTAAACTTCGCTAGCCGTGTTCGGCG


Block sizes: 38 (upstream exon), 37 (downstream exon)
Score: 11

AAATTCTAAATTGACACACTTGCTGCAAGATTCTCTAGgtaagatgat ... ttggtaatagGAGGAGACTCAAAAGCATTGATGTTTGTGCAAATTAGCCCATCCGATAATGATGTTTCGGAAACATTGAGTTCACTAAACTTCGCTAGCCGTGTTCGGCG


Block sizes: 38 (upstream exon), 37 (downstream exon)
Score: 14

AAATTCTAAATTGACACACTTGCTGCAAGATTCTCTAGgtaagatgat ... ttggtaatagGAGGAGACTCAAAAGCATTGATGTTTGTGCAAATTAGCCCATCCGATAATGATGTTTCGGAAACATTGAGTTCACTAAACTTCGCTAGCCGTGTTCGGCG


Block sizes: 38 (upstream exon), 34 (downstream exon)
Score: 12

AAATTCTAAATTGACACACTTGCTGCAAGATTCTCTAGgtaagatgat ... ttggtaatagGAGGAGACTCAAAAGCATTGATGTTTGTGCAAATTAGCCCATCCGATAATGATGTTTCGGAAACATTGAGTTCACTAAACTTCGCTAGCCGTGTTCGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctcacttggccacatgattaattttctttatgtgcttttgccattggtaatagGAGGAGACTCAAAAGCATTGATGTTTGTGCAAATTAGCCCATCCGATAATGATGTTTCGGAAACATTGAGTTCACTAAACTTCGCTAGCCGTGTTCGGCG
               atgattaattttcttt  TA-rich tract