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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTGCTGGTACGGGTGGTTCTATGCTTATCATTGGCTCTGCAGCAGGTGTGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaacttttactctaataataagtggagctgtggaacaacttacacaatacagaatcgtatgttacagaacaagaaacttattcggtgtggttg...

Basic information

species Oryza sativa
transcript LOC_Os09g02214.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g02214.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G053927_T02 (Zea mays), 5'ss of exon 9
CTGTGCTGGTACGGGTGGTTCTATGCTTATCATTGGCTCTGCAGCAGGTGTGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaacttttactctaataataagtggagctgtggaacaacttacacaatacaga-atcgtatgttacagaacaagaaacttattcggtgtggttg
|||||| ||||| |||||||| ||||||||||||||||| |||||||| || ||||| |||||| |||| ||||||||||||||||||||||| |||||||||||  |  | |||  || ||||  ||| | | || |  || ||  || |  | |  || ||    |  |  |  |    |  | | |    | |   ||
CTGTGCGGGTACTGGTGGTTCAATGCTTATCATTGGCTCCGCAGCAGGAGTTGCTTTTATGGGAGTGGAGAAGGTGGATTTCTTTTGGTATTTTCGCAAGgtaaacggctcctttg-tcaaatatgaagagaaactatctaaaaagatatattacagcgatatgaagttctttattatggtagccatgtgaaatttaactg

upper sequence: LOC_Os09g02214.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA10G40920.1 (Glycine max), 5'ss of exon 9
CTGTGCTGGTACGGGTGGTTCTATGCTTATCATTGGCTCTGCAGCAGGTGTGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaacttttactctaataataa-gtggagctgtggaacaacttacacaatacagaa-tcgtatgttacagaacaagaaacttattcggtgtggttg
 ||||||||||| ||||| || ||| | || |||||||| || || || || || |||||||| |||||||||||||| ||||||||||| || || ||||||  |   ||| |     ||| | | |  ||  | |    |  || |||      |||||| || | |||  |        |                   
TTGTGCTGGTACTGGTGGATCCATGTTAATTATTGGCTCAGCTGCTGGAGTTGCGTTCATGGGGATGGAAAAGGTGGACTTCTTTTGGTACTTACGAAAGgtatttcctactctacacataagacttatatgatgtttgtaagtaatttatg----acagaagtcatttgtctcctttttgcag------------------

upper sequence: LOC_Os09g02214.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA20G26380.1 (Glycine max), 5'ss of exon 9
------------CTGTGCTGGTACGGGTGGTTCTATGCTTATCATTGGCTCTGCAGCAGGTGTGGCTTTCATGG-GAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaacttttactctaataataagtggagctgtggaacaacttacacaatacagaatcgtatgttacagaacaagaaacttattcggtgtggttg
             ||||||||||| ||||| || ||| | || |||||||| || || || || || ||||||| | |||||||||||||| ||||||||||| || || ||||||  |   ||    || |  |  |  | | | | ||   ||    ||   |  |||| | |  | | |  |       | |                  
GTTGATTGCATTTTGTGCTGGTACTGGTGGATCCATGTTAATTATTGGCTCAGCTGCTGGAGTTGCGTTCATGGAGGATGGAAAAGGTGGACTTCTTTTGgtacttacgaaaggtatttcctacacg-acacataagactaattgtgttgataaaatgtttgtgcg-taca-agtaatttatctccatttttgcag-----------------

upper sequence: LOC_Os09g02214.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA20G26550.1 (Glycine max), 5'ss of exon 7
CTGTGCTGGTACGGGTGGTTCTATGCTTATCATTGGCTCTGCAGCAGGTGTGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaacttttactctaataataagtggagctgtggaacaact-tacacaatacagaatcgtatgttacagaacaagaaacttattcggtgtggttg
 |||||| |||| || || || ||  | || |||||||| || || || || || |||||||| |||||||||||||| ||||||||||| || || ||||||  |   ||| | || || | |   | ||  |   |  ||    | | || | | ||     |   |     |   | |    || | | |        
ATGTGCTAGTACTGGCGGATCCATATTAATTATTGGCTCAGCTGCTGGAGTTGCGTTCATGGGGATGGAAAAGGTGGACTTCTTTTGGTACTTACGGAAGgtacttcctactgt-acacttagacatattgatgtgataaaatgtttgtgcatagttca----tgagagacctcgtttatgtcctttttgcag--------

upper sequence: LOC_Os09g02214.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT3G19490.1 (Arabidopsis thaliana), 5'ss of exon 9
CTGTGCTGGTACGGGTGGTTCTATGCTTATCATTGGCTCTGCAGCAGGTGTGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaacttttac------tctaataataagtgg---agctgtggaacaacttacacaatacagaat---cgtatgttacagaacaagaaacttattcggtgtggttg------------
|||||| || || |||||||| |||||| ||||||| ||||| || ||||| || |||||||| ||||| || || |||||||||||||||||||| |||||||  |  | | || |      |||||  || |       | |  || |  |||       | ||  |||   | | ||   | |  ||||||||| | |   | |  ||             
CTGTGCCGGCACTGGTGGTTCGATGCTTGTCATTGGTTCTGCTGCTGGTGTAGCCTTCATGGGGATGGAGAAAGTCGATTTCTTTTGGTATTTCCGAAAGgtaagatacattcttccggcttgtctaacgatcaacaacacaacattgcattaaccagactgaaactcaatactcttgtggctctgcgcaagaaactcagttttttttttttttctccatgcag

upper sequence: LOC_Os09g02214.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv03s0180g00120.t01 (Vitis vinifera), 5'ss of exon 9
CTGTGCTGGTACGGGTGGTTCTATGCTTATCATTGGCTCTGCAGCAGGTGTGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaacttttactctaataataagtggagctgtggaacaacttacacaatacagaatcgtatgttacagaacaagaaacttattcggtgtggttg-
 ||||||||||||||||| || |||||  | ||||||||||| || || || || || ||||| |||||||| ||||| ||||||||||| ||  | ||||||   ||  ||      ||  || |   ||    |  ||    | |||   ||    ||| | |   |||  |||  ||||| |  |||  | |      
TTGTGCTGGTACGGGTGGATCCATGCTAGTTATTGGCTCTGCTGCTGGAGTTGCATTTATGGGGATGGAAAAAGTGGACTTCTTTTGGTACTTAAGGAAGgta---tgtgctgcggtgctgctatttgatgataattcggttttaatta---aaattggaaactttccttagtgaa--agaaattgtttccttttatgcag

upper sequence: LOC_Os09g02214.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S298_28V6.1 (Physcomitrella patens), 5'ss of exon 9
CTGTGCTGGTACGGGTGGTTCTATGCTTATCATTGGCTCTGCAGCAGGTGTGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgta---aattgaactt---ttactctaataataagtggagctgtggaacaa---cttacacaatacaga-------atcgtatgttacagaacaagaaacttattcggtgtggttg-------------------------------------------------------
 |||||||| || ||||||||||| ||| ||||||||||||| || |||||||| | |||||| |||||||| |  || ||||| |||||| |    ||||||   |  || | ||   || || |   | | |   |   |||  || ||   |||   | |    ||       |    | || |||  |||  | |  | ||    ||| ||                                                        
TTGTGCTGGAACTGGTGGTTCTATTCTTGTCATTGGCTCTGCTGCGGGTGTGGCCTACATGGGCATGGAAAAAGCTGACTTCTTATGGTATCTAAAAAAGgtatgaatctgcatttatcttgctttttcatttatctgtattgtataaaaaatccttgttcgaggtcgatgatttgaaaacaggtcacaacacagtagagattttgaccgtgattttgttttattgctcttgcatgcttggtatcaaatagtgattctttttatatggcag

upper sequence: LOC_Os09g02214.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S246_109V6.1 (Physcomitrella patens), 5'ss of exon 9
CTGTGCTGGTACGGGTGGTTCTATGCTTATCATTGGCTCTGCAGCAGGTGTGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaacttttactctaataataagtggagctgtggaacaacttacacaatacagaatcgtatgtta--cagaacaagaaacttattcggtgtggttg----------------------------------------------------------------
||||||||| || ||||||||||| ||||||||||||||||| |||||||| || | |||||| |||||||| |  || ||| | |||||  |    |||||||   ||||    | |    |  |  ||    |||||    |  | | |   ||     |||  |||||    ||| || |   ||      ||  |  |                                                                
CTGTGCTGGAACAGGTGGTTCTATCCTTATCATTGGCTCTGCTGCAGGTGTCGCCTACATGGGCATGGAAAAAGCCGACTTCCTATGGTACCTGAAAAAGgtaa---gaaccagcatttgcctttttcgtttttctgtgttgtagataaaagtttatgttctcgcttgttaacttgaataacaggttttgataatggaggcgctttattccgaatacttgtgttctcttgcagttggtgttaaacgagaattgttttttttggcag

upper sequence: LOC_Os09g02214.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ32271 (Selaginella moellendorffii), 5'ss of exon 7
CTGTGCTGGTACGGGTGGTTCTATGCTTATCATTGGCTCTGCAGCAGGTGTGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaacttttactctaataataagtggagctgtggaacaacttacacaatacagaatcgtatgttacagaacaagaaacttattcggtgtggttg
||| || || || || ||||| ||||| ||||| ||||| ||||| ||||| ||||||||||| ||||||||||  || ||||| ||||| ||    ||||| |  |   || || |||   |    | |        ||  ||||||      |      | ||                                   
CTGCGCCGGGACTGGCGGTTCAATGCTCATCATCGGCTCCGCAGCTGGTGTTGCTTTCATGGGGATGGAAAAGGCTGACTTCTTCTGGTACTTTAAGAAGgtgagatctcctctttctcgcgtttccatt-------cggctcaacttcgtttttttttttttgtccag-------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86432129|gb|CI085740.1|CI085740
EST:     TTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAG                         GTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTTATCTA
genomic: TTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaa ... ggttttgcagGTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTTATCTA
EST: gi|86477900|gb|CI120533.1|CI120533
EST:     TGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAG                         GTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTTATCTA
genomic: TGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaa ... ggttttgcagGTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTTATCTA
EST: gi|16578636|gb|BI812731.1|BI812731
EST:     T-GCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGC-AG                         GTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTTATCTA
genomic: TGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaa ... ggttttgcagGTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTTATCTA
EST: gi|88844788|gb|CI021363.1|CI021363
EST:     TGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAG                         GTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTTATCTA
genomic: TGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaa ... ggttttgcagGTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTTATCTA
EST: gi|86524663|gb|CI164869.1|CI164869
EST:     ATTTCCGCAAG                         GTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATTATCACTTATCTA
genomic: ATTTCCGCAAGgtaaattgaa ... ggttttgcagGTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTTATCTA
EST: gi|86413982|gb|CI068189.1|CI068189
EST:     TTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAG                         GTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTGATCTA
genomic: TTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaa ... ggttttgcagGTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTTATCTA
EST: gi|88972218|gb|CI018665.1|CI018665
EST:     TGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAG                         GTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTTATCTA
genomic: TGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaa ... ggttttgcagGTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTTATCTA

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: 61 (upstream exon), 70 (downstream exon)
Score: 16

CTGTGCTGGTACGGGTGGTTCTATGCTTATCATTGGCTCTGCAGCAGGTGTGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaa ... ggttttgcagGTGAGTGGTTTTGCCCTTGCAGGTTATGCAGCTGGTATCATCACTTATCTAGCTGCACAAAATCTCCCTCTATCCCTTCCCACTTCACTAGCCGAGATCC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTGCTGGTACGGGTGGTTCTATGCTTATCATTGGCTCTGCAGCAGGTGTGGCTTTCATGGGAATGGAAAAGGTGGATTTCTTTTGGTATTTCCGCAAGgtaaattgaacttttactctaataataagtggagctgtggaacaacttacacaatacagaatcgtatgttacagaacaagaaacttattcggtgtggttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA