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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctaagtcttttagttttccatgttgaatatcatcaccattttcaactattaaacctacaattagctgacatttcttgtcatgtttttactttttagGCTGCTTGTGAAGATCTTAGAGGCAGTAGGTTGTTCCTAAAACTCCTTGAAGCAGTGCTGAGAACCGGAAACCGGATGAATGTTGGGACAAATAGGGGTG

Basic information

species Oryza sativa
transcript LOC_Os03g10680.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g10680.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G075921_T01 (Zea mays), 3'ss of exon 3
-----------------------gtatgctaagtctt--ttagttttc--catgttgaatatcatcaccattttcaac-----tattaaacc-tacaattagctgacattt-------cttgtcatgtttttactt---tttagGCTGCTTGTGAAGATCTTAGAGGCAGTAGGTTGTTCCTAAAACTCCTTGAAGCAGTGCTGAGAACCGGAAACCGGATGAATGTTGGGACAAATAGGGGTG
                        |    |||  |||  ||   || |  ||| |||| ||  | ||  ||     ||     ||| || ||  ||       | | | ||       | |  ||| | || ||||   || |||| || || |||||||| |||||||| ||||||||||| ||||| || || || |||||||||||||| |||||||||||||| || |||||  ||||||
gtacgctaaaatggtaatccatgctgcattaatccttctttcacttccatcattttgattactaacattatcactgacctgtgtatcaatccacaccgcagatttagacttataggtgcctaacatttcttcacttgttttcagGCAGCCTGCGAAGATCTCAGAGGCAGCAGGTTGTTCCTGAAACTACTCGAGGCGGTGCTGAGAACCGGGAACCGGATGAATGTCGGCACAAACCGGGGTG

upper sequence: LOC_Os03g10680.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G872264_T01 (Zea mays), 3'ss of exon 4
----------------------------------gtatgctaagtcttttagttttccatgttgaa--tatcatcaccattttcaactattaaacctacaa--ttag-ctgacattt-cttgtcatgtttttactt---tttagGCTGCTTGTGAAGATCTTAGAGGCAGTAGGTTGTTCCTAAAACTCCTTGAAGCAGTGCTGAGAACCGGAAACCGGATGAATGTTGGGACAAATAGGGGTG
                                   |  | | | |    |  ||||      |||   ||||||   | | |  | | ||  || || ||   |||| || | |  | | |   || | || ||||   || |||| || || ||||||||||||||||| ||||||||||| ||||| || ||||||||||||||||| || ||||||||||||||||| |||||  ||||||
gtacgctaaaatggtaactgatgctgcattgatccttcgttcacttccatcattttgatcagtgacattatcattgacctgtgtatcaatcgaaactccagatttagactaataggtacctaagatttcttcacttgttttcagGCAGCCTGCGAAGATCTTAGAGGCAGCAGGTTGTTCCTGAAACTGCTCGAAGCAGTGCTGAGAACTGGGAACCGGATGAATGTTGGCACAAACCGGGGTG

upper sequence: LOC_Os03g10680.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv07s0129g00220.t01 (Vitis vinifera), 3'ss of exon 3
gtatgctaagtcttttagttttccat--gttgaatatca--tcaccattttcaactattaaacctacaattagctgacatttcttgtcatgtttttacttt-ttagGCTGCTTGTGAAGATCTTAGAGGCAGTAGGTTGTTCCTAAAACTCCTTGAAGCAGTGCTGAGAACCGGAAACCGGATGAATGTTGGGACAAATAGGGGTG
        | |  | ||| ||   |   | |  | ||||  |  | ||  |      ||||    | || ||      |   ||  | || ||   | ||| | |||| ||  |||| ||  | |    |||  |  ||||||| |||||||||||||| || || || || ||||| || ||||||||||| || || |||||||
---cctggaatagtgtagattagaaatggctacagatcaattgtctatacttgttccttaag---agaactattcatgagacctcattatcttccaaatttgtcagGCAGCAAGTGAGGAATTGAAGAACAGCCGCCTGTTCCTTAAACTCCTTGAAGCTGTTCTCAGGACAGGAAATCGAATGAATGTTGGCACCAACAGGGGTG

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: 27 (upstream exon), 70 (downstream exon)
Score: 3

GGATATACCTTTTGCCTTCAAAAGAGTTGATGCAATGCTATACCGAGCCAATTTTGAGACTGAAATAAATTACCTAAGAAACTCTTTTGAAACTCTGGAGgtatgctaag ... tactttttagGCTGCTTGTGAAGATCTTAGAGGCAGTAGGTTGTTCCTAAAACTCCTTGAAGCAGTGCTGAGAACCGGAAACCGGATGAATGTTGGGACAAATAGGGGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaactattaaacctacaattagctgacatttcttgtcatgtttttactttttagGCTGCTTGTGAAGATCTTAGAGGCAGTAGGTTGTTCCTAAAACTCCTTGAAGCAGTGCTGAGAACCGGAAACCGGATGAATGTTGGGACAAATAGGGGTG
                     agctgac  putative branch site (score: 3)
                                       tgtttttacttttt  putative PPT
                                      atgtttttacttttta  TA-rich tract