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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgtttggacattttgtaagttgtcggtttataatttttgtgccaaataatcatcaaaccatatgctaaaaatccag

Basic information

species Oryza sativa
transcript LOC_Os01g49690.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G055905_T03 (Zea mays), 5'ss of exon 5
CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgttt--ggacattttgtaagttgtcggtttataatttttgtgccaaataatcatcaaaccatatgctaaaaatccag
||| |||||||| || ||||||||||| || || |||||||||||||||||||| ||||||||||| |||||||| || |||||||||||||||||    ||||||   | |  ||| |   |  | ||| ||   | ||  | | |  || |    | |   |||  |||||||    || |||
CTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCATTAATGGTCAAgtaagtacctctagggaaaaaatacaggttttcatatcatgctatctcggcaagtctacc--taaattatatgctgg--attcag

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G518717_T03 (Zea mays), 5'ss of exon 1
CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgttt---ggacattttgtaagttgtcggtttataatttttgtgccaaataatcatcaaaccatatgctaaaaatccag
||| |||||||| || || |||||||| || || ||||||||| |||| ||||| ||||||||||| |||||||| || ||||||||||||||||||   |||||||  |||   | | |  ||  | ||| |    | ||  || || || ||||| ||  | |||  |||||  |  ||| |||
CTATGATGAGTGTCAGAGAAAGTATGGCAACGCCAATGCATGGAGGTACTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCATTAATGGCCAAgtaagttcctttatggaaaaaattacatgttcttatgtcatg-ttattttggcaaatcatacttaaattatatg--acgaattcag

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G43470.1 (Glycine max), 5'ss of exon 5
CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgtttgga---cattttgtaagttgtcggtttataat----ttttgtgccaaataatcatcaaaccatatgctaaaaatccag-------------------------------------------------------------------
 || ||||| ||||| ||||||||||| ||||| ||||| ||||||||||| || ||||| ||||||||||| |||||||| ||||| ||| |||| || |||| | | |||      |   |  | |  | ||  |     ||     | |||||    |  |    |    |   | |  |  |  |                                                                    
TTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTACCTAACTCTTTCTGCAATTATTGATGGAACTgtaaatatctttcactccctcctcttcaagtatctatcccccatgtgcctctgtgcatcttggtgggtagcttactggatttattttgactttttatagttctgtttgaatggttcttgttcaaaattaagttttatatatgttatgtttgacccag

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G23310.4 (Glycine max), 5'ss of exon 5
CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgtttgga---cattttgtaagttgtcggtttataat----ttttgtgccaaataatcatcaaaccatatgctaaaaatccag-------------------------------------------------------------------
 || ||||| ||||| ||||||||||| ||||| ||||| ||||||||||| || ||||| ||||||||  | || ||||| ||||| ||| |||| || |||| | | |||      |   |  | |  | ||        ||     | |||||    |  |    |    |   | |  |  |  |                                                                    
TTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTATTGATGGAACTgtaaatatcttttactccctcctcttcaagtatctaccccccatgtgcctctgtgcatcttggtgggtagcttactggatttattttgactttttgttgttctattagaatgttgcttgttcaaaattgagttttctatatgctatgcttgacccag

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G23310.2 (Glycine max), 5'ss of exon 5
CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgtttgga---cattttgtaagttgtcggtttataat----ttttgtgccaaataatcatcaaaccatatgctaaaaatccag----------
 || ||||| ||||| ||||||||||| ||||| ||||| ||||||||||| || ||||| ||||||||  | || ||||| ||||| ||| |||| || |||| | | |||      |   |  | |  | ||        ||     | |||||    |  |    |    |   | |  |  |  |           
TTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTATTGATGGAACTgtaaatatcttttactccctcctcttcaagtatctaccccccatgtgcctctgtgcatcttggtgggtagcttactggatttattttgactttttgttgt

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 5
CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgtttggacattttgta--agttgtcggtttataatttttgtgc-caaataatcatcaaaccatatgctaaaaatccag-----------------------------------------------------
 || ||||| ||||| ||||||||||||||||| ||||| ||||| ||||| || |||||||||||||| ||||||||||| ||||| ||  |||| || |||| | | |||  ||  | |  |  |||  ||    |||  || || ||  ||  ||  ||     | |  |  |   | |  |                                                      
TTATGATGAATGCCAGAGGAAGTATGGGAATGCTAATGCTTGGCGATATTGTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctctttttactctctccatcagtcctcctcctatttttcttatgtgcatgtaggcagtggtcaaggtttttttattttattttgaattctgtttgaaaataactaagtcttttatttgctctggttcacttag

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 5
CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagt--ttgtttggacattttgtaagttgtcggttt--ataatttttgtgccaaataatcatcaaaccatatgctaaaaatccag
||| || || ||||| ||||||||||| || || ||||| ||||| |||||||| |||||||||||||| ||||| || ||||| || ||  ||||||| ||||||  ||  || |  | || | |  |||| | |    | |  | | |    |  | ||  | |||   | ||||     || ||
CTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTATAGATGGCACAgtaagtgatttcttagcaacttggca--ttgttgatgagaacacatatagctgtatgttatactaaaatagtttgcttt--gtctag

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 5
CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgtttggacattttgtaagttgtcggtttataatttttgtgccaaataatcatcaaaccatatgctaaaaatccag-------------------------------
||| || || ||||||||||||||||| ||||| ||||| ||| | |||||||| |||||||||||||| ||||| |||||||| || ||  ||||||| |||||| | | |   | | ||     |||| | | |    | ||  ||   |||  | || ||  |||| | ||    |  |                                
CTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTATAGATGGCACTgtaagtatttctcagcttctttggcattgt-gttatgatgtgttcttgtataatt-ttatgaatgcataagttagctgtataccatattaaaacgtattgcatcctcaatgtag

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 5'ss of exon 5
CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgt----ttggacattttgtaagttgtcggtttataatttttgtgccaaataatcatcaaaccatatgctaaaaatccag----------------------------------------------
||| ||||||||||| |||||||| || ||||| |||||||||||||| ||||| ||||||||||||||||| || || || || || ||  |||| || ||||   | |    ||     | |  |   ||      |   | | | ||||        |         ||||    ||  |  ||                                              
CTATGATGAGTGCCAGAGGAAGTACGGAAATGCTAATGCATGGCGGTACTGCACAGATGTTTTTGACTACCTAACCCTCTCTGCGATAATAGATGGAACTgtaaacctctcactttatctctctcttgcattaatctgtaccagtgtgtgtgtgtgtgtgtgtgtttttaatatatctaagttgtagtgtctatctgttaatgttatatgtctcattgtttttggaattccag

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S31_220V6.1 (Physcomitrella patens), 5'ss of exon 5
CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagttt---gtttggacattttgtaagttgtcggtttataatttttgtgccaaataatcatcaaaccatatgctaa-aaatccag---------------
 || ||||| || ||  | |||||||| ||  | ||||| |||||||||||||| || |||||||||||||| || || || || |||||  |||| | |||||  ||     ||| ||  ||   |   |||| || | || | ||    ||| ||  ||   |||     |  |   | |||                  
TTATGATGAATGTCAGCGTAAGTATGGAAACCCAAATGCTTGGCGGTATTGCACTGACGTTTTTGACTACCTGACACTCTCGGCTATCATAGATGGAAGGgtaaagttcaaacttgcacggttaa-attctgtccgtgtgta-tgttcaacccagattttcgataaagagcctcttggtagatctcatcgtgctgtaggatt

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S207_36V6.1 (Physcomitrella patens), 5'ss of exon 5
CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaag-------tttgtttgg--acattttgtaagt-tgtcggtttataatttttgtgccaaataa---tcatcaaaccatatgctaaaaatccag-----
 || || || |||||  |||||||||| ||  | ||||| |||||||| ||||| |||||||||||||||||||| || ||||| || ||  |||| | ||||||        ||   |||  | || |||   || |||| ||||| | ||| |||    |  |      ||||    || |  | |   |  ||     
TTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAATAGATGGAAGGgtaagggggaaacttacgtggttaaatattgcttgtatgtctgttta-actttatgttttgagaagagtctatcagtagatgtcatcatggttgaggatta

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|58588304|gb|CF986612.1|CF986612
EST:     GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACG                         GTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
genomic: GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgt ... aaaaatccagGTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
EST: gi|218484413|gb|FG953190.1|FG953190
EST:     GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACG                         GTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
genomic: GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgt ... aaaaatccagGTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
EST: gi|24468838|gb|CA305787.1|CA305787
EST:     GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACG                         GTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
genomic: GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgt ... aaaaatccagGTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
EST: gi|27577318|gb|CB000013.1|CB000013
EST:     GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACG                         GTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
genomic: GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgt ... aaaaatccagGTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
EST: gi|431829|gb|D23910.1|D23910
EST:     CTTTCAGCAATCATTAATGGCACG                         GTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
genomic: CTTTCAGCAATCATTAATGGCACGgtaagtttgt ... aaaaatccagGTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
EST: gi|27577630|gb|CB000325.1|CB000325
EST:     GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACG                         GTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
genomic: GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgt ... aaaaatccagGTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
EST: gi|27577051|gb|CA999745.1|CA999745
EST:     GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACG                         GTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
genomic: GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgt ... aaaaatccagGTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
EST: gi|27334364|gb|CA882815.1|CA882815
EST:     GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACG                         GTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
genomic: GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgt ... aaaaatccagGTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
EST: gi|51946060|gb|CV152401.1|CV152401
EST:     GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACG                         GTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
genomic: GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgt ... aaaaatccagGTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
EST: gi|29686455|gb|CB682730.1|CB682730
EST:     GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACG                         GTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG
genomic: GCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgt ... aaaaatccagGTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG

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: 75 (upstream exon), 51 (downstream exon)
Score: 56

CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgt ... aaaaatccagGTTCTTTGTGTTCATGGTGGACTTTCTCCTGATGTGCGCACTGTTGATCAG




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