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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattgtgtgctccatgcaagaatttttattttgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacag

Basic information

species Oryza sativa
transcript LOC_Os06g05180.2
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 15
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattgtgtgctccatgcaagaatttttattttgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacag---------------
||||||| | |||||||||||| | || || || |||||||||||||||||||| |||||||| ||||| |||||||| || |||||||||||||| |||||| |||| || |||||      | ||  ||| || ||||  |  ||| |||||    | | ||  ||    |  | || |     ||  | | ||| |                
TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatagtctgctc-----gaaaacatttcttctgtt--taaattctctatatgggcacttcatgt--catgacttcaattgcttacatagttataagctttatacttacag

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G095348_T03 (Zea mays), 5'ss of exon 15
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattgtgtgctccatgcaagaatttttattttgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacag---------------
||| ||||| |||||||||||| | || || || |||||||||||||||||||| |||||||| || |  |||||||| || |||||||||||||| |||||| | || || | |||| || || |  |||| || |||| | ||  | | ||| |    | ||||||    || | || |     ||  ||| ||| |                
TCACGAGGTCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCGTTGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaaaatagtctactccttg-aaaacgttttcttctgtttaagttctctatatggc--cactttgtgagtcacgacttcaattgtttacacagttataagctttgtacttacag

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA13G43680.1 (Glycine max), 5'ss of exon 15
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattgtgtgctccatgcaagaatttttattttgttaa----tgtattttctattgtagt---attttgtgcactacaaatttatcccgttgtacatttacag---------
 |||||  | ||||| || ||  | ||||| ||||||||||| || |||||||| || |||||||| || ||| | || || || ||||||||||| |||||||  | | | |  ||| | | ||| || |  |||    ||    |||   |||| || || |   | |    | |  |  |    |||  | || | | | |            
ACATGAAATGAATGAACGTGTCAGAACAGGCATCTGGGTTGGGGATTGCTTTATCTACAACAATTCCTCTTGGAGACTTAATTACTGTGTTGGTGGTGAGgtattaactcttt--tcccttctagatttctagtttaaaaaagaattgtgcattcttttttaattgaactacaaggatcatgagac-atcttgatgcataatgattatgaatttag

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 15
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattgtgtgctcc-----atgc--aagaatttt-tattttgttaatgtattttctattgtagtattttgt--gcact-acaaatttatcccgttgtacatttacag--------------------------------------------------
||||||  | ||||| || ||  ||||||||||||||||||| || || ||||| || |||||||| || ||| | || ||||||||||||||||| ||||||| || | | | | |      || |  ||||  |   |||||  ||| || | | | | || |  | |||| |  |   | |  ||||| |    | ||| |||||  |                                                  
TCATGAAATGAATGAACGTGTCAGGACAGGGATCTGGGTTGGGGATTGTTTTATCTACAACAATTCTTCTTGGAGGCTTAACTATTGTGTTGGTGGTGAGgtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatat-gtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttag

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 4
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattgtgtgctcc-----atgcaagaa---tttttattttgttaatgtattttctattgtagtattttgtgca-ctacaaatttatcccgt-tgtacatttacag--------------------------------------------------
||||||  | ||||| || ||  ||||||||||||||||||| || || ||||| || | |||||| || ||| | || ||||||||||||||||| ||||||| |||  | | | |      || ||| |    | | |||||  ||| || | | ||  |  |  | |||| |    || ||    | ||   | |||| |||||  |                                                  
TCATGAAATGAATGAACGTGTCAGGACAGGGATCTGGGTTGGGGATTGTTTTATCTACAGCAATTCTTCTTGGAGGCTTAACTATTGTGTTGGTGGTGAGgtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttag

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 15
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattgtgtgctccatgcaagaatttttattttgttaa-------tgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacag---------
 |||||  | ||||| || ||  ||||||| ||||||||||| || |||||||| || |||||| | || ||| | || || || ||||||||||| |||||||  | | | |  ||| | | ||| || |  |||    ||       || ||| | | |  | | | |  | | |  |  |    |||  | |  | | | |            
ACATGAAATGAATGAACGTGTCAGGACAGGCATCTGGGTTGGGGATTGCTTTATCTACAACAATACCTCTTGGAGACTTAATTACTGTGTTGGTGGTGAGgtattaactcttt--tcccttctagatttctagtttaaaaaaagaattgtgcattctttttaattgaactacgaggatcatgagac-atcttgatacataatgattatgaatttag

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 15
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 15
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattgtgtgctccatgcaagaatttttattttgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacag
 || |||  | |||| || ||  |||| || || |||||||| |||||||| ||||| ||||| || || |||   || |||||||||||||| |||||||||   |        || ||       ||||  || |  | || | || |    |  | ||| |  |   || | ||| || || || | |         
CCACGAGAATGATGAACGTGTTAGGACCGGTATATGGGTTGGGGACTGCTTCATTTACAACAACTCTTCTTGGAAGCTTAACTATTGTGTTGGAGGCGAGgtactca----agagtctat-------ttttatttctaatcatct-ttatgagctacattatataata-gctgctaatata-cctgtggcag--------

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 15
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 15
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtat---atattgtgtgctc----catgcaagaatttttattt-tgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacag
 ||||||   |||||  ||||  | || || || |||||||||||||| || ||||| ||||| || || ||||| || || || |||||||||||||||||||    ||||||   | |    | || ||| ||||  || | ||   |||   |   | |  | |  || |  |  ||      |||        ||  ||  |||
CCATGAGACAAATGAAAGAGTTAGAACTGGTATATGGGTTGGAGACTGTTTCATTTACAACAACTCCTCTTGGCGGCTTAATTACTGTGTTGGTGGCGAGgtattgtgtattgtccacccttgtcttgaaagtatttccatatgtgcagatgatatccatttcatggatttcttggagcttttttgttaaataaccatatgttc-cag

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 15
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 15
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattgtgtgctccatgcaagaatttttattttgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacag
 |||||  | |||||||||||  | || || || |||||||| |||||||| ||||| || || || || ||||| || ||||||||||||||||| ||||||||       || | |  |   | |||| ||| |   | || |   |||||  ||    |  | |  | |   ||| |      ||            
CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttgattccaggttgtatttctatatatatgatcttcattctaaggtgcagtcatataaattgttaatgtgatgatttcag---------

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 15
lower sequence: PP1S79_180V6.2 (Physcomitrella patens), 5'ss of exon 15
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtat---atattgtgtgctccatgcaagaatttttattttgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacag
 || ||  |    || ||| |  | || ||  | ||||| || |||||||| ||||| ||||||||  ||||| | || ||||||||||| ||||| ||||||    | |    ||   || |  |   | | | |||| | |  | |       ||  | || ||    | ||||  |    | ||  | ||    |     
ACACGAAATCTCCGAACGAATTAGAACTGGCTTGTGGGTGGGCGACTGCTTCATTTACAACAATTCGGCATGGAGGCTCAACTATTGTGTCGGTGGAGAGgtaaggaaaaacaagtaaaccttagacacaatgtcattt-gcttctttgaaggtgatctttgtgttgctcgaactagtagaccaccctctggtgagatggt--

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 15
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 5'ss of exon 15
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattgtgtgctccatgcaagaatttttattttgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacag-----
 || ||  ||  ||||||| |  | || ||  | |||||||| |||||||| ||||| ||||||||| ||||| | || ||||| ||||||||||| ||||||  || || ||  | ||||   ||     || |     |  ||||   | |||  ||    | ||  | ||||  |||| |   |     | || ||      
GCACGAAATTCCTGAGCGAATTAGAACTGGCTTGTGGGTTGGTGACTGCTTCATTTACAACAATTCAGCATGGAGACTCAACTACTGTGTTGGTGGAGAGgtaagtaatg-gtcatacatgatggatcagctaatgctgcaccgtat---ccatttcagatactagtagattacat-tttagcttatgagttacttgcatccaat

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|58660118|gb|CK048798.1|CK048798
EST:     TTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAG                         GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTG
genomic: TTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattg ... acatttacagGTCACCACGATGTATCACTTGGATCGCCCTATGTACTTG
EST: gi|58690875|gb|CK079562.1|CK079562
EST:     TTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAG                         GTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTA
genomic: TTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattg ... acatttacagGTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTA

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: 66 (upstream exon), 72 (downstream exon)
Score: 21

TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattg ... acatttacagGTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattgtgtgctccatgcaagaatttttattttgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG