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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcggtttcctgatgttaggtgtatgaattgaacacattgctatattgcagctagtgaaatgactggatcatggttctcttattttcagGAGATAAGTTTCAAGAGTAAACCAAATGTTTGGGCCTATTTCTCAGTAAAG

Basic information

species Oryza sativa
transcript LOC_Os05g22940.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 10
------gtgcggtttcctgatgttaggtgtatgaattgaacacat-----tgctatatt-gcagctagtgaaatgactggatcatggttctcttattttcagGAGATAAGTTTCAAGAGTAAACCAAATGTTTGGGCCTATTTCTCAGTAAAG
      ||    | ||   |  || | | | | ||| | | | ||     || |  |||      | || | |||||  | || ||||| |  |||||| ||||||||||||| || || || || |||||||||||||| ||||||||||||
tccatggtata-tatctaaagtttggatcttttaatggtatagatccaattgttccatttatgtttggttacatgaccaggtcttggtttttatatttt-agGAGATAAGTTTTAAAAGCAAGCCTAATGTTTGGGCCTACTTCTCAGTAAAG

upper sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM5G858094_T02 (Zea mays), 3'ss of exon 10
gtgcggtttcctgatgttaggtgt-atgaattgaacacattgctatattgcagctagtgaaatgactggatcatggttctcttattttcagGAGATAAGTTTCAAGAGTAAACCAAATGTTTGGGCCTATTTCTCAGTAAAG
||  | ||||  |||   | || | ||  || |  || |     | |||     | || |||||||| | || || || | |   ||||||||||||||||| || || || || |||||||||||||| ||||||||||||
gtaagttttctagatcacatgtattatatatcgttcaaag----agattaagtttggttaaatgactaggtcttgattttttatctttcagGAGATAAGTTTTAAAAGCAAGCCTAATGTTTGGGCCTACTTCTCAGTAAAG
















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 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 74 (downstream exon)
Score: 55

TGAAGTAGATTCTAAATGGCCAAAAGGCCACTGCGTAGCTGTTAGAATAACTAGCGAGGATCCAGATGATGGGTTTAAGCCTACTGGTGGAAAAGTAAAGgtgcggtttc ... ttattttcagGAGATAAGTTTCAAGAGTAAACCAAATGTTTGGGCCTATTTCTCAGTAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattgctatattgcagctagtgaaatgactggatcatggttctcttattttcagGAGATAAGTTTCAAGAGTAAACCAAATGTTTGGGCCTATTTCTCAGTAAAG
                                        ttctcttattttc  CT-rich tract
                                           tcttatttt  TA-rich tract