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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtatctgatagatacttttttcactgttcaaacattatgattttggttttaccagtcctcacaatactgatattttcttatgtgtttcaacagTGAAAAAGATCAAGCTGAGAACTTGATGATTGTTGACCTCCTAAGAAACGATCTTGGTAAGGTTTGTGAACCTGGGAGTGTGCATGTTCCTCGCCTCATG

Basic information

species Oryza sativa
transcript LOC_Os06g48620.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g48620.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G416386_T01 (Zea mays), 3'ss of exon 13
gcaagtatctgatagatactt---ttttcactgttcaaacattatgattttggttttaccagtcctcacaatactgatattttcttatgtgttt-----caacagTGAAAAAGATCAAGCTGAGAACTTGATGATTGTTGACCTCCTAAGAAACGATCTTGGTAAGGTTTGTGAACCTGGGAGTGTGCATGTTCCTCGCCTCATG
       | | || | ||  |   | |||    | | ||   | |      |   | |   |      | ||| |     |||   ||||| |      || ||| |||||||| || || |||||| |||||||||| |||||| ||||||||||||| || ||||| || || || ||||| |||||||| || |||||||||
-----agtttcattgttatctggatgttctaaatgctaatcctgtttcacagcgctcatatgctactgctatattttcccttttgcatgtgctcaactccaccagCGAAAAAGACCAGGCCGAGAACCTGATGATTGTCGACCTCTTAAGAAACGATCTCGGCAAGGTCTGCGAGCCAGGGAGCGTGCATGTCCCACGCCTCATG

upper sequence: LOC_Os06g48620.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA20G31970.1 (Glycine max), 3'ss of exon 15
gcaagtatctgatagatacttttttcac-tgttcaaacattatgattttggtt-ttaccagtcctcacaat--actg-atattttcttatgtgtttcaacagTGAAAAAGATCAAGCTGAGAACTTGATGATTGTTGACCTCCTAAGAAACGATCTTGGTAAGGTTTGTGAACCTGGGAGTGTGCATGTTCCTCGCCTCATG
  || |||   |||   |   || | || ||||  | ||      | |   ||  |  ||||      |||    ||   | |  |||   |  |    ||| ||||| ||||| ||||| |||||||||||||||||||| ||||| || || |||||    || ||||| |||||   ||| ||||| || || ||||||
--aaatattgaatacccagaattgtaacgtgttagagcaaagcactctaacttgctttcagtggggtgaatctgttgtgaactaacttgctttctctttcagCGAAAAGGATCAGGCTGAAAACTTGATGATTGTTGACCTTCTAAGGAATGACCTTGGCCGTGTCTGTGATCCTGGATCTGTTCATGTGCCACGTCTCATG

upper sequence: LOC_Os06g48620.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv13s0019g04170.t01 (Vitis vinifera), 3'ss of exon 12
-gcaagtatctgatagatacttt-tttcactgttcaaacattatgatttt---ggttttaccagtc-ctcacaatactgatattttcttatgtgtttcaacagTGAAAAAGATCAAGCTGAGAACTTGATGATTGTTGACCTCCTAAGAAACGATCTTGGTAAGGTTTGTGAACCTGGGAGTGTGCATGTTCCTCGCCTCATG
  ||| ||||| ||  | ||  | |||    || |||| || || |||||    |  | |   ||  |   | |||     | | |||  |     ||||||||||||||||||| ||||| ||  ||||||||||||| || |||||||| || ||||||   || |||||||||||   | | ||||||||| | || |||
tacaaatatctaatgaagacaatgtttttgagtccaaaaataataatttttaaagcctaatatgttgcctgccataaactaactctctctt---cctcaacagTGAAAAAGATCAGGCTGAAAATCTGATGATTGTTGATCTTCTAAGAAATGACCTTGGTCGTGTCTGTGAACCTGGATCTATTCATGTTCCTTGTCTTATG

upper sequence: LOC_Os06g48620.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv13s0019g04180.t01 (Vitis vinifera), 3'ss of exon 11
---gcaagtatctgatag-atacttttttcactgttcaaacattatgattttggttttaccagtcctca---caatactgatattttcttatgtgtttcaacagTGAAAAAGATCAAGCTGAGAACTTGATGATTGTTGACCTCCTAAGAAACGATCTTGGTAAGGTTTGTGAACCTGGGAGTGTGCATGTTCCTCGCCTCATG
     |  ||| |  | |  ||| |     ||  ||      |||||||||| |  |     ||    |    || ||  |   | | | || | | | ||||||||||| ||||| ||||| || |||||||||||||| || || || ||  |||| |||   || || ||    ||   ||||||||| || |  ||||||
aatctagctattttttggtgtacgtgcaatacaattt---tgttatgatttttgcatgcattgtttgtaaactaacacgtacgctctttaat-tatctgaacagTGAAAAGGATCAGGCTGAAAATTTGATGATTGTTGATCTGCTGAGGAATAATCTGGGTCGTGTCTGCGAGGTGGGTTCTGTGCATGTACCCCTTCTCATG

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: 68 (upstream exon), 51 (downstream exon)
Score: 23

ACCGAAATGCAATTCTGGAAGCAAAGCCAATCAAAGGTACTATAGCACGTGGCAGAACACCAGAGGAAGATGAATGCCTACGTTTGCAGTTGAAATACAGgcaagtatct ... gtttcaacagTGAAAAAGATCAAGCTGAGAACTTGATGATTGTTGACCTCCTAAGAAACGATCTTGGTAAGGTTTGTGAACCTGGGAGTGTGCATGTTCCTCGCCTCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttggttttaccagtcctcacaatactgatattttcttatgtgtttcaacagTGAAAAAGATCAAGCTGAGAACTTGATGATTGTTGACCTCCTAAGAAACGATCTTGGTAAGGTTTGTGAACCTGGGAGTGTGCATGTTCCTCGCCTCATG
                          tactgat  putative branch site (score: 23)
                        aatactgatatttt  TA-rich tract