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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggttttcatctccatcttcttcttcctcttcaatgccattgccagccgtttcgatcgattcgtctccattaaaccttgctgatattgtgatactgacaagtggcgtgcatgcatccatccatgcagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT

Basic information

species Oryza sativa
transcript LOC_Os10g42490.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G123140_T04 (Zea mays), 3'ss of exon 2
gtacggttttcatctccatcttctt--cttcctcttcaatgccattgccagccgtttcgatcgattcgtctccattaaaccttgctgatattgtgatactgacaagtggcgt-gcatgcatc-catccatgcagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT
||| |     ||  |  ||   |||  |||    |  |     ||   |  |   | ||||  |||    ||  |||    | ||    || |  ||    |     ||| | ||| | |   ||| |   |||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||||||||||| 
gtaagacacacacatatatacgcttgccttttcatatataataataatcttcttctccgatatattataatctcttacggat-gcatgcatggcaatggcaatggccggcattgcacggacgacatacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAGCTGGGGCTCAAACCCCGCCAGGTCAAGTTCTGGTTCCAGAAC

upper sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G01850.1 (Glycine max), 3'ss of exon 2
gtacggttttcatctccatcttcttcttcctcttcaatgccattgccagccgtttcgatcgattcgtctccattaaaccttgctgatattgtgatactgacaagtggcgtgcatgcatccatccatgcagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT
        |  |||||  |||| |  ||||| |   ||   | ||  |        |||| |   || |  |||     ||| |   |||||     | |   ||   ||     |||        ||||  |||||||||| ||||| || || || || |||||| ||||||| |||||||| ||| |||| || ||||| |||||||||||||||||||||||||| 
--------tagatctctctcttttgtttcctttgtgataaaactgaaa------ctgatcaa--ggttttaatttgttgttgtt--cattgt----ttcatgtgtaatgta---acatttg-----gcagTTTGTTCAAGGAATGCCCACACCCTGATGATAAGCAGAGGCTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC

upper sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G34070.1 (Glycine max), 3'ss of exon 2
gtacggttttcatctccatcttcttcttcctcttcaatgccattgccagccgtttcgatcgattcgtctccattaaaccttgctgatattgtgatactgacaagtggcgtgcatgcatccatccatgcagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT
                       |   |  |  |   |  ||||   |    | |   | ||    ||    |  || |||  |  |  | |   ||| |  | |  |   | |  ||   |    ||||  |||||||||| || || || ||||| || |||||| | ||||| |||||||| ||| |||| || ||||| |||||||||||||||||||||||||| 
----------------------ataaatattaattgttagcattattatttttgtaagttgaaaattcgaactgcaatcttttt--tcctttatcactaa--actaac---cttatatttttttg-gcagTTTGTTCAAGGAATGTCCACACCCGGATGATAAGCAGAGACTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC

upper sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0012g02030.t01 (Vitis vinifera), 3'ss of exon 2
gtacggttttcatctccatcttcttcttcctcttcaatgccattgccagc-cgtttcgatcg--attcgtctccattaaaccttgctgatattgtg-atactgaca----agtggcgtgcatg-catccatccat-gcagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT
     || | |  ||   |||   ||   ||||||||   ||| |         ||| |||   |  | |  |   ||||  |||   | ||     | ||| |||    ||| ||      | ||  |||   | ||||  | |||||||| ||||| || || || ||||||||| || |||| || ||||| ||||| ||||||||||| ||||| |||||||| |||||||| || 
-----gtatgctactatttctctctcactctcttcaaaaacatggttcttatacttcaatcacaacccattacgcataaatgttgggaaaatcacctaaactcacactctagttgcaccaccgtcactcattttttgcagTTTATTCAAGGAATGCCCACACCCAGATGACAAGCAGAGGATGAAACTCAGCCAAGAACTTGGCCTCAAACCACGCCAAGTCAAGTTTTGGTTCCAAAAC

upper sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ37532 (Selaginella moellendorffii), 3'ss of exon 1
gtacggttttcatctccatcttcttcttcctcttcaatgccattgccagccgtttcgatcgattcgtctccattaaaccttgctgatattgtgatactgacaagtggcgtgcatgcatccatccatg---cagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT
                                                                                 |    || ||  |  |       ||  | | |   |||  ||   |   |||| ||||||||||||| || ||||| ||||| |||||||| | | ||||||||| ||| || || ||  | ||||| || |||||||||||||||||||||
---------------------------------------------------------------------------------gtaagtactgcaagccgagagcatgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT

upper sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ10492 (Selaginella moellendorffii), 3'ss of exon 2
gtacggttttcatctccatcttcttcttcctcttcaatgccattgccagccgtttcgatcgattcgtctccattaaaccttgctgatattgtgatactgacaagtggcgtgcatgcatccatccatgcagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT
                                                         |  |||| || |   |      ||   |||     |      |   |     |   | | |     |  ||||  ||||||||||||||||||||||||| ||||||||||||| | |||| |||| ||| || ||  |  | || || || |||||||| ||||||||||||
------------------------------------------------------gtaagagattggttttggt--gttgttctcgattggaagtcctcaaggtggattttttcttcgttttctcgcgcagCTTGTTCAAGGAGTGCCCGCATCCGGATGACAAGCAGCGGCAGGAGCTCAGCCGGGAGCTCGGATTGGAGCCGCGGCAAGTCAAGTTTTGGTTCCAGAAT

upper sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
gtacggttttcatctccatcttcttcttcctcttcaatgccattgccagccgtttcgatcgattcgtctccattaaaccttgctgatattgtgatactgacaagtggcgtgcatgcatccatccatg---cagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT
                                                                                 |    || |   |  |       ||  | | |   |||  ||   |   |||| ||||||||||||| || ||||| ||||| |||||||| | | ||||||||| ||| || || ||  | ||||| || |||||||||||||||||||||
---------------------------------------------------------------------------------gtaagtactacaagccgagagcatgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT

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: 50 (upstream exon), 28 (downstream exon)
Score: 2

AGCCGCCCGACGCCGCCCAGCCCAGCGGCGCCGCGGGGGGCAACGCCAAGAAGAAGCGCTACCACCGCCACACGGCGCACCAGATCCAGCAGATGGAGGCgtacggtttt ... atccatgcagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccttgctgatattgtgatactgacaagtggcgtgcatgcatccatccatgcagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT
                   tactgac  putative branch site (score: 2)
                                          tccatcc  putative PPT
        tgatatt  TA-rich tract