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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACATGTAACAGGGAAAGATGCTCTTGGTAAGCCTGGAAAGATAGCATCTTATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAGgtaatagcaggcattgttttgctggtggcttccagctttctgttgtccattgctaagctgagactcttgtactcaactttcag

Basic information

species Oryza sativa
transcript LOC_Os03g46740.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g46740.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G868168_T02 (Zea mays), 5'ss of exon 8
TACATGTAACAGGGAAAGATGCTCTTGGTAAGCCTGGAAAGATAGCATCTTATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAGgtaatagcaggcattgttttgctggtggcttccagctttctgttgtccattgctaagctgagactcttgtactcaactttcag
| ||| | || ||    ||||| ||||| ||||| ||||| ||||| || ||||| ||||| || ||||||||||||||||||| | |||| ||||| |||||  |  |   | || |   ||  |  || |  |   || |||||| ||||||  | ||  | |||  || |    ||||||
TGCATATGACTGGACGGGATGCCCTTGGCAAGCCAGGAAAAATAGCTTCCTATGTTGTTGTGACCCATCAGCATAGCACAATAAGAAGAGCTGTTGATAGgta--aagaacaaatgctacacttttcactccatgacctcagttgtctattgctgggttggta-tctgatatttgcttttcag

upper sequence: LOC_Os03g46740.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv04s0023g00290.t01 (Vitis vinifera), 5'ss of exon 8
TACATGTAACAGGGAAAGATGCTCTTGGTAAGCCTGGAAAGATAGCATCTTATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAGgtaatagcaggcat--------tgttttgctggtggcttccagctttct----gttgtccattgctaagctgagac---tcttgtactcaactttcag-------------
| ||| ||| || | ||||||| | ||| |||| ||| ||||| ||||| ||||| |||||||||||||| ||||| || || | | |||||||||||||||| |       |         ||  || |||   |      ||||| |      | |   | |||  | |  |||   || |  |||  | |  ||              
TCCATTTAAAAGAGGAAGATGCACCTGGGAAGCTTGGGAAGATTGCATCATATGTAGTTGTCACTCATCAACATAGTACCATTAGAAGAGCCGTTGACAGgtagtgcttcatacaaatgagatgcatttctgaaagtacaaggctttgtcaggaatttatgtggctttgttctgacatatcctaaact-gattgccattgttattatatag
















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|38476994|gb|CF961127.1|CF961127
EST:     TATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAG                         GTTGTTATTTCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATGACACAAGA
genomic: TATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAGgtaatagcag ... caactttcagGTTGTTATTTCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATGACACAAGA
EST: gi|27921057|gb|CB096865.1|CB096865
EST:     TATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAG                         GTTGTTATTCCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATGACACAAGA
genomic: TATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAGgtaatagcag ... caactttcagGTTGTTATTTCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATGACACAAGA
EST: gi|58691671|gb|CK080358.1|CK080358
EST:     TATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAG                         GTTGTTATTTCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATGACACAAGA
genomic: TATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAGgtaatagcag ... caactttcagGTTGTTATTTCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATGACACAAGA
EST: gi|88508239|gb|CI435745.1|CI435745
EST:     TCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAG                         GTTGTTATTTCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATGACACAAGA
genomic: TCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAGgtaatagcag ... caactttcagGTTGTTATTTCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATGACACAAGA
EST: gi|58593744|gb|CF992052.1|CF992052
EST:     TATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAG                         GTTGTTATTTCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATGCACACAAG
genomic: TATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAGgtaatagcag ... caactttcagGTTGTTATTTCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATG-ACACAAG
EST: gi|27547660|gb|CA767399.2|CA767399
EST:     TATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAG                         GTTGTTATTTCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATGACACAAGA
genomic: TATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAGgtaatagcag ... caactttcagGTTGTTATTTCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATGACACAAGA

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), 59 (downstream exon)
Score: 16

TACATGTAACAGGGAAAGATGCTCTTGGTAAGCCTGGAAAGATAGCATCTTATGTGGTTGTCACTCATCAGCATAGCACAATAAAACGAGCCGTTGACAGgtaatagcag ... caactttcagGTTGTTATTTCTCCATGAGGGGAAGGTAGTGTGGGAAGGAATGACACAAGAATTTACTACATCAACAAATCCTATTGTAAAACAG




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