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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgttaggattaatatttctcaacacctgattctacttttatagaaatttggtgtgatacttttcagtaaagcaactaaatttagtttttttttggtagGCTCTTGATACTTTCAACACAGCAGTTGTATCACCGATATACTATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAG

Basic information

species Zea mays
transcript GRMZM2G110398_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110398_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g65986.1 (Oryza sativa), 3'ss of exon 6
gatgttaggattaatatttctcaacacctgattctacttttatagaaatttggtgtgatacttttcagtaaagcaactaaatttagt---ttttttttggtagGCTCTTGATACTTTCAACACAGCAGTTGTATCACCGATATACTATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAG
    | ||| || ||||   |  |   ||| | | |  |  ||     |   ||   |||    |   ||||    ||||  ||| |   |||  |||   |||||||||| || ||||| || |||||||| || || ||||| ||||||||||| || |||||||||||||||||||| |||||||||||||||
--actcaggcttgatatacatgcatgactg-tacaatgtccatcactttacagttcaatatagcttgttaaatgccctaagcttactctgtttccttttacagGCTCTTGACACATTCAATACTGCAGTTGTTTCGCCTATATATTATACAATGTTTACATCACTAACCATTTTGGCTAGTGTGATAATGTTCAAG
















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: 48 (upstream exon), 48 (downstream exon)
Score: 95

GACCTTTTCTGGCATGAATCAGCTAATTTATCCACAAACATGGTTGTTCACCATTGTTGTTGTTGCATGTATAGTAACACAGATGAACTACCTGAACAAGgtaatactga ... tttttggtagGCTCTTGATACTTTCAACACAGCAGTTGTATCACCGATATACTATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

GACCTTTTCTGGCATGAATCAGCTAATTTATCCACAAACATGGTTGTTCACCATTGTTGTTGTTGCATGTATAGTAACACAGATGAACTACCTGAACAAGgtaatactga ... tttttggtagGCTCTTGATACTTTCAACACAGCAGTTGTATCACCGATATACTATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

GACCTTTTCTGGCATGAATCAGCTAATTTATCCACAAACATGGTTGTTCACCATTGTTGTTGTTGCATGTATAGTAACACAGATGAACTACCTGAACAAGgtaatactga ... tttttggtagGCTCTTGATACTTTCAACACAGCAGTTGTATCACCGATATACTATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 133

GACCTTTTCTGGCATGAATCAGCTAATTTATCCACAAACATGGTTGTTCACCATTGTTGTTGTTGCATGTATAGTAACACAGATGAACTACCTGAACAAGgtaatactga ... tttttggtagGCTCTTGATACTTTCAACACAGCAGTTGTATCACCGATATACTATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatttggtgtgatacttttcagtaaagcaactaaatttagtttttttttggtagGCTCTTGATACTTTCAACACAGCAGTTGTATCACCGATATACTATACAATGTTCACGTCACTAACCATTTTGGCTAGCGTGATAATGTTCAAG
                             aactaaa  putative branch site (score: 133)
                                    tttagttttttttt  CT-rich tract
                       taaagcaactaaattt  TA-rich tract