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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgatatgtttgacatttttgtaaaatttccttagCCTACTTTATATGGAATGTTCATTGTCAAAAATGTGGTTCGTACATTCTAATTCCTCTTTAGAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAA

Basic information

species Zea mays
transcript GRMZM2G085747_T05
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085747_T05 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 9
gtatctgatatgtttgacatttttgtaaaatttccttagCCTACTTTATATGGAATGTTCATTGTCAAAAATGTGGTTCGTACATTCTAATTCCTCTTTAGAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAA---------------------------------------------------------------------
|||| |||||||||||| ||  ||| |   ||   | ||  || || |||     | ||  ||||||||| | || ||| | | ||||||||||||||||||||||||||||||||||||||||||||  |||||||||                                                                     
gtatatgatatgtttgatatgcttgcatttttctatcagtttatttcatacaaggtatttcttgtcaaaagtctgtttcctccgttctaattcctctttagaatccagTGCTGGGATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCCAGGGATAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGAC
















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), 47 (downstream exon)
Score: 284

CTGGAGTTGCTCTAGCAGGCCTACTTGGTGCTGTTAGAGCACAGGGCCGTCCTCTCCAGGATTTTACGAATCAAAAGATAGTCGTTGTGGGAGCTGGAAGgtatctgata ... atttccttagCCTACTTTATATGGAATGTTCATTGTCAAAAATGTGGTTCGTACATTCTAATTCCTCTTTAGAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

CTGGAGTTGCTCTAGCAGGCCTACTTGGTGCTGTTAGAGCACAGGGCCGTCCTCTCCAGGATTTTACGAATCAAAAGATAGTCGTTGTGGGAGCTGGAAGgtatctgata ... atttccttagCCTACTTTATATGGAATGTTCATTGTCAAAAATGTGGTTCGTACATTCTAATTCCTCTTTAGAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

CTGGAGTTGCTCTAGCAGGCCTACTTGGTGCTGTTAGAGCACAGGGCCGTCCTCTCCAGGATTTTACGAATCAAAAGATAGTCGTTGTGGGAGCTGGAAGgtatctgata ... atttccttagCCTACTTTATATGGAATGTTCATTGTCAAAAATGTGGTTCGTACATTCTAATTCCTCTTTAGAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 128

CTGGAGTTGCTCTAGCAGGCCTACTTGGTGCTGTTAGAGCACAGGGCCGTCCTCTCCAGGATTTTACGAATCAAAAGATAGTCGTTGTGGGAGCTGGAAGgtatctgata ... atttccttagCCTACTTTATATGGAATGTTCATTGTCAAAAATGTGGTTCGTACATTCTAATTCCTCTTTAGAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatctgatatgtttgacatttttgtaaaatttccttagCCTACTTTATATGGAATGTTCATTGTCAAAAATGTGGTTCGTACATTCTAATTCCTCTTTAGAATCCAGTGCTGGGATAGGTGTGCTTAGCATGGCTAAA
                           gtttgac  putative branch site (score: 128)
                                              tttcctt  putative PPT
                            tttgacatttttgtaa  TA-rich tract