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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCATAGCTGGAGCTTATCAAGGATTTCAGAGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAGgtcagtccacatatatatattctacctcggtttctgttaacacgctttttaaattactgaacggtgggttttgtgtaaaaactttatatatataagttcc...

Basic information

species Oryza sativa
transcript LOC_Os01g58640.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g58640.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G007754_T01 (Zea mays), 5'ss of exon 7
CTGCATAGCTGGAGCTTATCAAGGATTTCAGAGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAGgtcagtccacatatatatattctacctcggtttctgttaacacgctttttaaattactgaacggtgggttttgtgtaaaaactttatatatataagttcc----
 || | |  ||||||||||||||  ||||||| || || ||||||||||| ||||| || | |  ||||||| ||||||||||||||     ||| |   |||    |||     | ||  | | | ||| | ||   ||||    |   ||||   |   |  |     || | | |  |    
TTGAACAAGTGGAGCTTATCAAGAGTTTCAGAATTCGGGTATGCCAGGGTGCATGCCACAAGAGGTGATATGCTGGTTCAGgtcagtttttgtatttcctttccttttcg--caatattttctctcctttcacatgtttgaatta-gtactttggagattgatgtggggcat-tgaataacgaaa

upper sequence: LOC_Os01g58640.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AC207043.3_FGT004 (Zea mays), 5'ss of exon 7
CTGCATAGCTGGAGCTTATCAAGGATTTCAGAGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAGgtcagtccacatatatatattctacctcggtttctgttaacacgctt-tttaaattactgaacggtgggttttgtgtaaaaactttatatatataagttcc------------------------------------------------------------------
 || | |  ||||||||||||||  ||||||| || || ||||||||||| ||||| || | |  ||||||| ||||||||||||||     ||| |   ||   |     ||||| |     | | | ||| ||||| |     | | | || ||||      || |   |   || |||                                                                   
TTGAACAAGTGGAGCTTATCAAGAGTTTCAGAATTCGGGTATGCCAGGGTGCATGCCACAAGAGGTGATATGCTGGTTCAGgtcagtttttgtatttccttttcgcaatattttctctcctttcacatgtttgaattagtactttg-gagattggtgtggggcattgaataacgaaaattctagaaaattcagaaagagggccatttgggcatttcactctgaacaattgttaatctctcttcttcag

upper sequence: LOC_Os01g58640.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AC209374.4_FGT007 (Zea mays), 5'ss of exon 6
CTGCATAGCTGGAGCTTATCAAGGATTTCAGAGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAGgtcagtccacatatatatattctacctcgg-----tttctgttaacacgctt-tttaaattactgaacggtgggttttgtgtaaaaactttatata-tataagttcc------------------------------------------------------------------
 || | |  ||||||||||||||  ||||||| || || ||||||||||| ||||| || | |  ||||||| ||||||||||||||     ||| |   |||    |||      ||||| |     | | | ||| ||||| |     | | | ||  |||     | ||  |||    || | ||                                                                  
TTGAACAAGTGGAGCTTATCAAGAGTTTCAGAATTCGGGTATGCCAGGGTGCATGCCACAAGAGGTGATATGCTGGTTCAGgtcagtttttgtatttcctttccttttcgcaatattttctctcctttcacatgtttgaattagtactttg-gagattaatgtgggggcattgaataacgaaaataccagaaaattcagaaagagggccatttgggcatttcactctaaacaattgttaatctctcttcttcag

upper sequence: LOC_Os01g58640.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G138756_T01 (Zea mays), 5'ss of exon 3
CTGCATAGCTGGAGCTTATCAAGGATTTCAGAGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAGgtcagt-ccacatatat-atattctacctcggtttctgttaacacgctttttaaattactgaacggtgggttttgtgtaaaaactttatatatataagttcc
  | |   |||||||||||||||| |||| |||||||| |||| || ||| ||||| || | ||| |||||| |||||||||| ||| || ||| | |  | |||   | |  | | | ||| || | || | |     |  ||   ||   |   || | |||    || |  | | |||  
GGGGAGGCCTGGAGCTTATCAAGGGTTTCGGAGTTTGGCTATGGCAAGGTGCATGCTACAAGAACCGATATGCTGGTTCAGgtgagttccccatgtgttgtgttccggcccc-tctattttagcatgtttataagtactccaaatattgaagtggttgaataaataaaat-tccacaggttaa

upper sequence: LOC_Os01g58640.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G326625_T01 (Zea mays), 5'ss of exon 8
CTGCATAGCTGGAGCTTATCAAGGATTTCAGAGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAGgtcagtccacatatatatattctacctcggtttctgttaacacgctttttaaattactgaacggtgggttttgtgtaaaaactttatatatataagttcc--------------------------------------------------------------------------------------------
  | |   ||||||||||||||||||||| |||||||| |||| || ||| ||||| || | ||| |||||| ||||||||||  || |       | |||| || |  | ||     ||   |   | || || |  |  |   |   |    |   | |  || | | |  ||| |  |                                                                                            
GGGGAGGCCTGGAGCTTATCAAGGATTTCGGAGTTTGGCTATGGCAAGGTGCATGCTACAAGAACCGATATGCTGGTTCAGgtgtgttccggcccctctattttagcatgtttataagtactccaaatattgaagtggttga--atcaataaaattccacaggttaacacacctaattctcagcaaatgttgaaaaagaaacaccactttagttttaaaaatggttctgcatttgcatggaagtctgaataattgttaacctctttcattcag

upper sequence: LOC_Os01g58640.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G138698_T03 (Zea mays), 5'ss of exon 12
CTGCATAGCTGGAGCTTATCAAGGATTTCAGAGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAGgtcagtccacatatatatattctacctcggtttct----gttaacacgctttttaaattactgaa-cggtgggttttgtgtaaa---aactttatata-tataagttcc------------------------------------------------------------------
 || | |  ||||||||||||||  ||||||| || || ||||||||||| ||||| || | |  ||||||| ||||||||||||||     ||| |   ||     ||  | | |     ||  | | ||||| | ||   ||||   ||   ||     |  |     | ||  |||    || ||||                                                                  
TTGAACAAGTGGAGCTTATCAAGAGTTTCAGAATTCGGGTATGCCAGGGTGCATGCCACAAGAGGTGATATGCTGGTTCAGgtcagtttttgtatttccttttcctttccttctttcaatattctctcccttttcacatgtttgaaatagtactttacagattgatgtggcattggataacgaaaattccagaaaattcagaaagaacgccatttgggcatctccctctgaacaattgttactctattttcttcag

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|88661250|gb|CI450540.1|CI450540
EST:     ATGTTGGTTCAG                         TTTGTAAACTCGAACACGTCGGCAGTCCAGGACCAATTTAGGATTGTGAAG
genomic: ATGTTGGTTCAGgtcagtccac ... cttttttcagTTTGTAAACTCGAACACGTCGGCAGTCCAGGACCAATTTAGGATTGTGAAG
EST: gi|58593137|gb|CF991445.1|CF991445
EST:     AGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAG                         TTTGTAAACTCGAACACGTCGGCAGTCCAGGACCAATTTAGGATTGTGAAG
genomic: AGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAGgtcagtccac ... cttttttcagTTTGTAAACTCGAACACGTCGGCAGTCCAGGACCAATTTAGGATTGTGAAG
EST: gi|87015622|gb|CI277580.1|CI277580
EST:     AGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAG                         TTTGTAAACTCGAACACGTCGGCAGTCCAGGACCAATTTAGGATTGTGAAG
genomic: AGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAGgtcagtccac ... cttttttcagTTTGTAAACTCGAACACGTCGGCAGTCCAGGACCAATTTAGGATTGTGAAG
EST: gi|66915919|gb|CX102767.1|CX102767
EST:     AGTTTGGATATGCCAGTGTACATGCGACGAAAACTGATATGTTGGTTCAG                         TTTGTAAACTCGAACACGTCGGCAGTCCAGGACCAATTTAGGATTGTGAAG
genomic: AGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAGgtcagtccac ... cttttttcagTTTGTAAACTCGAACACGTCGGCAGTCCAGGACCAATTTAGGATTGTGAAG
EST: gi|88661254|gb|CI450562.1|CI450562
EST:     TGATATGTTGGTTCAG                         TTTGTAAACTCGAACACGTCGGCAGTCCAGGACCAATTTAGGATTGTGAAG
genomic: TGATATGTTGGTTCAGgtcagtccac ... cttttttcagTTTGTAAACTCGAACACGTCGGCAGTCCAGGACCAATTTAGGATTGTGAAG
EST: gi|29668284|gb|CB664559.1|CB664559
EST:     AGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAG                         TTTGTAAACTCGAACACGTCGGCAGTCCAGGACCAATTTAGGATTGTGAAG
genomic: AGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAGgtcagtccac ... cttttttcagTTTGTAAACTCGAACACGTCGGCAGTCCAGGACCAATTTAGGATTGTGAAG

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: 39 (upstream exon), 54 (downstream exon)
Score: 6

CTGCATAGCTGGAGCTTATCAAGGATTTCAGAGTTTGGATATGCCAGGGTACATGCGACGAAAACTGATATGTTGGTTCAGgtcagtccac ... cttttttcagTTTGTAAACTCGAACACGTCGGCAGTCCAGGACCAATTTAGGATTGTGAAGGGAGCCAGATGATCCAACCTTACAAGCAACTTGATATTCACAAGGAGAA




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