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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaagcttattgcctgctcttgtttccgtatctgtgattcagcattatgtgccatgcttaactgtacaggttggtctcctgtggcaccatataccattctaacttcaagtaactctgtaccaattgcag

Basic information

species Oryza sativa
transcript LOC_Os02g53140.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G104920_T03 (Zea mays), 5'ss of exon 12
CAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaagcttattgcctgctcttgtttccgtatctgtgattcagcattatgtgccatgcttaactgtacaggttggtctcctgtggcaccatataccattctaacttcaagtaactctgtaccaattgcag
|||||| ||||| ||||||||||||||||||||  ||||||| || || || || ||||| || || ||||| || ||||||||||||||||| ||||||||||| |||||||| |  |||| || |||| || |       || ||   |||||     ||  | | | ||    |   ||   || ||  ||  |  | |  || | | ||                      
CAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTGTTTATCACAAGgtaatggcaagcttctgtcctggtcatgttcccatg--cagcatgcattgttatgatgtgtgactcaatata---atcaatcagatg-ggttcctaactctacactgattgcag---------------------

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 14
CAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaagcttattgcctgctcttgtttccgtatctgtgattcagcattatgtgccatgcttaactgtacaggttggtctcctgtggcaccatataccattctaacttcaagtaactctgtaccaattgcag
|||||||||||| |||||||||||||| |||||  ||||||| || || ||||| ||||| || || |||||||| ||||||||||||||||| ||||||||||| |||||||| | || || ||||||| ||||       || ||   ||| |     || || ||  |   | |  ||    ||||   | | |   ||  ||   | ||                      
CAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAGgtaatcgcaagcttctggcttggtcttgttcccgtg--cagcatgcattgttacgatgtgtgattcacctt---gatcagtaagatgtgttccta-acttcacactggttgcag---------------------

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S264_64V6.1 (Physcomitrella patens), 5'ss of exon 13
CAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaagcttattgcctgctcttgtttccgtatctgtgatt-cagcattatgtgccatgcttaactgtacaggttggtctcctgtggcaccatataccattctaacttcaagtaactctgtaccaattgcag
 ||||| || |  || |||||||| ||||||||||| ||||| || |  || || || |  || || |||| ||| |||||||| |||||||||||||||||||      | || |     |  || ||   | |   ||||||    | ||  | ||   |    ||||   || ||     ||   |     | | | |   |                               
GAGAGGACATACCAACGAAAAGAATTTTGTTGGGCTATCTGTTAACAGTGAATATATAGGTTGTGGTAGTGTAACAAATGAGGTGTTTGTTTACCACAAGgtaacgttttgtttctgtttagtactagtgcacat---tgtgatcgtggaatcttttgttttttacaactt--caagtaaacttctgtttatgacctttgcttgt-------------------------------

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S37_28V6.1 (Physcomitrella patens), 5'ss of exon 12
CAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgta--attgcaagcttattgcctgctcttgtttccgta-tctgtgattcagcattatgtgccatgcttaactgtacaggttggtctcctgtggcaccatataccattctaacttcaagtaactctgtaccaattgcag----------------
  |||| ||||  ||||||||||| ||||| |||||  |||||||||  || ||||| || || || ||||||||||  ||||||||||| || |||||||||    |  |       |  |  |  ||||  || || | |||  ||||   || ||     |  ||     ||  |    | | |||| |  ||  | | || |||  |||   | | |||||  |||||  ||                  
TGGAGGACACACCAATGAAAAGAATTTTGTGGGGCTTACTGTAAATAGTGACTACATCGCTTGTGGCAGTGAAACGAGCGAGGTTTTTGTATATCACAAGgtatggctatagataagattacatcctttgtagccctagtttgtttttcacttttctgaatttt-tttgttgatattgaagtgccacctgggttactcttttcc-ttccgactgtgaatcactct-caccaagcgctttctgtttgtaccacag

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S154_52V6.1 (Physcomitrella patens), 5'ss of exon 12
CAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaagcttattgcctgctcttgtttccgtatctgtgattcagca-ttatgtgccatgcttaactgtacaggttggtctcctgtggcaccatataccattctaacttcaagtaactctgtaccaattgcag
|||||| ||||  ||||| ||||| ||||| ||  || ||||||| || ||||| |||||||||||||||||| | ||||||||||| || || || ||||| |   | ||  |  | | | | ||| || | |  ||  |||||   ||  | ||   ||   ||   | |         |||||  |   ||||    ||                                  
CAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCGTGTATCATAAGgttagacccagact-ctacatacactttttccagattcactgattgtacaactgtggtgcagattttgtttttgcaacatttctccaatt-taccagtctcc----------------------------------

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 5'ss of exon 12
CAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaagcttattgcctgctcttgtttccgtatctgtgattcagcattatgtgccatgcttaactgtacaggttggtctcctgtggcaccatataccattctaacttcaagtaactctgtaccaattgcag
 | ||| ||||  ||||||||||||||||||||  || |||| || | ||| ||||| ||||| || ||||||||||| ||||| ||||| || || |||||| |  |   || ||||  || ||| ||||    || |   ||| | ||| | ||  | || ||   | || |  | ||| |  | |  ||  |   |  | |  || ||                        
GAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACTGTCAACAGCGAATACATCGCCTGTGGCAGTGAAACGAACGAGGTGTTTGTGTATCATAAGgtattgtc---ctgattgtatgttctggtttt--aatttagaattta-catgacgtttcgtgttt---tttagaactcggttttgtata-catgaggcaa-agtgaaattt------------------------

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S25_325V6.1 (Physcomitrella patens), 5'ss of exon 12
CAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgca-agcttattgcctgctcttgtttccgtatctgtgattca--gcattat-gtgccatgcttaactgtacaggttg-------gtctcctgtggcaccatataccattctaacttcaagtaactctgtaccaattgcag-----------------
|||||| || |  ||||||||||| ||||| || ||| |||||||||| || |||||||| ||||| |||||||||||||||||  |||| ||||| |||||| ||  | |  | ||  |     |||| |   || |  |   |     |  || | || | ||| | || | |   ||  |       | | | |    ||   | |     ||  |||   |  |  | | |  ||  |                     
CAGAGGACATACCAATGAAAAGAATTTTGTAGGTCTGACTGTAAATAATGACTACATTGCTTGCGGCAGTGAAACGAATGAGGTCGTTGTGTACCATAAGgtatttctacaaatgatatcacatccttgctgtggtgtaggaagtgtgttgtgttttagttctatggtgaattttgttggacgttgaaatgccactttaaacaaactgttttcctccgactgggaaca-ttttatctcagatatttggtggtgttaatcacag

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ30221 (Selaginella moellendorffii), 5'ss of exon 11
CAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaagcttattgcctgctcttgtttccgtatctgtgattcagcattatgtgccatgcttaactgtacaggttggtctcctgtggcaccatataccattctaacttcaagtaactctgtaccaattgcag
 ||||| || | ||| |||||||||||||| ||||||||||| | |   || ||||| ||||| ||||| || || || ||||| | |||||||||||||||||        ||     ||||  ||||            ||   |   | |   |  ||| || |                                                                    
TAGAGGTCATACGAACGAAAAGAACTTTGTCGGGCTGTCTGTCACTTCTGATTACATCGCCTGTGGGAGCGAGACAAACGAGGTCTATGTTTACCACAAGgtaagcctggtttttagagctgca-ttgtcaagacgaagtagaacaaatctcaatggtgatgtttcag-------------------------------------------------------------------

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ24914 (Selaginella moellendorffii), 5'ss of exon 11
CAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaagcttattgcctgctcttgtttccgtatctgtgattcagcattatgtgccatgcttaactgtacaggttggtctcctgtggcaccatataccattctaacttcaagtaactctgtaccaattgcag
          | ||| |||||||||||||| ||||||||||| | |   || ||||| ||||| ||||| || || || ||||| | |||||||||||||||||   |    ||     ||||  |         |  |   |   | |   |||                                                                                
---------TACGAACGAAAAGAACTTTGTCGGGCTGTCTGTCACTTCTGATTACATCGCCTGTGGGAGCGAGACAAACGAGGTCTATGTTTACCACAAGGTAAGCCCGgtttttagagctgcattgtcaagacgaagtagaacaaatctcaatg--------------------------------------------------------------------------------

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|15856116|gb|BI808928.1|BI808928
EST:     AGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAG                         GCTATCTC-AAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
genomic: AGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaa ... ccaattgcagGCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
EST: gi|88248280|gb|CI248129.1|CI248129
EST:     AGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAG                         GCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
genomic: AGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaa ... ccaattgcagGCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
EST: gi|38476176|gb|CF960309.1|CF960309
EST:     AGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAG                         GCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
genomic: AGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaa ... ccaattgcagGCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
EST: gi|88220265|gb|CI219825.1|CI219825
EST:     CATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAG                         GCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
genomic: CATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaa ... ccaattgcagGCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
EST: gi|88906301|gb|CI375373.1|CI375373
EST:     AGTACAGTGCCTGCGGGAGTGAAACGAATGA-GTTTTTG-TTACCAC-A-                         GCTATCTCAAAACCTGCT-CCAACCACAGATTT-TATCATCTGATCTCGAT
genomic: AGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaa ... ccaattgcagGCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
EST: gi|29616392|gb|CB621404.1|CB621404
EST:     AGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAG                         GCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
genomic: AGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaa ... ccaattgcagGCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
EST: gi|86492605|gb|CI135238.1|CI135238
EST:     AGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAG                         GCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
genomic: AGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaa ... ccaattgcagGCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
EST: gi|86874566|gb|CI318125.1|CI318125
EST:     AAACGAATGAGGTTTTTGTTTACCACAAG                         GCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT
genomic: AAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaa ... ccaattgcagGCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGAT

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: 73 (upstream exon), 68 (downstream exon)
Score: 19

CAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaa ... ccaattgcagGCTATCTCAAAACCTGCTGCCAACCACAGATTTGTATCATCTGATCTCGATGATGCAGATGATGATCCTGGCTCTTATTTTATTAGCGCAGTCTGCTGGA




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