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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaacttattttgtgcataggtttaaaagcaatatgatgtgtttttatgattcattgcttttaactcctcaattccacagGTTATTGTTTTTGTTGATGCTTCTGAGGCTGATGAATTTTTAGAAGTTGCTTCGAAGCCTTTAGAATCATTACCATATGATTCTCCTGGGCAGACCTTTG

Basic information

species Zea mays
transcript GRMZM2G415729_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G415729_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 15
gtatgtaacttattttgtgcataggtttaaaagcaatatgatgtgtttttatgattcattgcttttaactcctcaattccacagGTTATTGTTTTTGTTGATGCTTCTGAGGCTGATGAATTTTTAGAAGTTGCTTCGAAGCCTTTAGAATCATTACCATATGATTCTCCTGGGCAGACCTTTG
|||    | || ||     ||    ||| |       || | ||| |||| |||  || || |||||  ||           ||||  | |||||||| |||||||||||||| |||||||||| |||||||||  ||||  | |||  ||| ||||| |||||||| || || || |||||||
gtaaacgattttttccactcagtatttttatttatggatta-gtgcttttctgaa-caatgtttttatttc-----------agGTGGTGGTTTTTGTGGATGCTTCTGAGGCCGATGAATTTTCAGAAGTTGCAACGAAATCATTAAGATCCTTACCTTATGATTCACCAGGACAAACCTTTG
















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), 49 (downstream exon)
Score: 170

GACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTACCAATACAATTCCTGAACAATTGCTTGAACAGgtatgtaact ... aattccacagGTTATTGTTTTTGTTGATGCTTCTGAGGCTGATGAATTTTTAGAAGTTGCTTCGAAGCCTTTAGAATCATTACCATATGATTCTCCTGGGCAGACCTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

GACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTACCAATACAATTCCTGAACAATTGCTTGAACAGgtatgtaact ... aattccacagGTTATTGTTTTTGTTGATGCTTCTGAGGCTGATGAATTTTTAGAAGTTGCTTCGAAGCCTTTAGAATCATTACCATATGATTCTCCTGGGCAGACCTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

GACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTACCAATACAATTCCTGAACAATTGCTTGAACAGgtatgtaact ... aattccacagGTTATTGTTTTTGTTGATGCTTCTGAGGCTGATGAATTTTTAGAAGTTGCTTCGAAGCCTTTAGAATCATTACCATATGATTCTCCTGGGCAGACCTTTG


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

GACTGAATACTCAGTTAATGTTGTGAAGCATATTTTTGATGGACATGTTGTGCTCCAATACAACTGTACCAATACAATTCCTGAACAATTGCTTGAACAGgtatgtaact ... aattccacagGTTATTGTTTTTGTTGATGCTTCTGAGGCTGATGAATTTTTAGAAGTTGCTTCGAAGCCTTTAGAATCATTACCATATGATTCTCCTGGGCAGACCTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagcaatatgatgtgtttttatgattcattgcttttaactcctcaattccacagGTTATTGTTTTTGTTGATGCTTCTGAGGCTGATGAATTTTTAGAAGTTGCTTCGAAGCCTTTAGAATCATTACCATATGATTCTCCTGGGCAGACCTTTG
                                 ttttaac  putative branch site (score: 133)
                                       ctcctca  CT-rich tract
                tttttatgattcatt  TA-rich tract