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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTAGGGAGGATTGCGGGATGGAGGCCAGCGCCGGGCTGGTCGCCGGCTCCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgcggcgctactgatttccggtgtctcgctctgcttggttgcctacttgctgctgatttttttgttcctctctctgtgtgtttgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g62090.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g62090.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G113137_T01 (Zea mays), 5'ss of exon 1
TGGTAGGGAGGATTGCGGGATGGAGGCCAGCGCCGGGCTGGTCGCCGGCTCCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgcggcgctactgatttccggtgtctcgctctgcttggttgcctacttgctgctgatttttttgttcctctctctgtgtgtttgtgcag
   | |    |   | ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| || ||||| ||||||||  |||  |||    |   | |   ||  | |    ||| ||| |    | || ||||||| || ||     ||                  
ATCTGGTAGCGCCAGGGGGATGGAGGCCAGCGCCGGGCTGGTCGCCGGCTCGCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGATGGCGAGCCAGGGgtacgtccgcctcgcc-tcgccctgctccgttcctcctcccttcgttcc----tcgccgctgattcttctgcctgcctgcag--------------
















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|58686350|gb|CK075037.1|CK075037
EST:     CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGG                         CCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|88342915|gb|CI640248.1|CI640248
EST:     CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGG                         CCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|58674902|gb|CK063589.1|CK063589
EST:     CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGG                         CCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|88441317|gb|CI602088.1|CI602088
EST:     CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGAGGGGGAGCCCGGG                         CCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|88764588|gb|CI773706.1|CI773706
EST:     CCCACAACCGGAACGAGCTCGTCGTCATCCGCCACGACGGGGAGCCCGGG                         CCGAAGCCGGTGAAACATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|88327372|gb|CI645156.1|CI645156
EST:     CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGG                         CCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|88727099|gb|CI750754.1|CI750754
EST:     CCCACAACCGGAACGACCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGG                         CCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|88317121|gb|CI626764.1|CI626764
EST:     CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGAAGGGGAGCCCGGG                         CCGAACCCGGTGAAGCATACGAATGGG
genomic: CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGTGAAGCATACGAATGGG
EST: gi|88314833|gb|CI608292.1|CI608292
EST:     CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGG                         CCGAAGCCGGT
genomic: CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGT
EST: gi|88334773|gb|CI647155.1|CI647155
EST:     CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGG                         CCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|88413432|gb|CI581447.1|CI581447
EST:     CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGG                         CCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|88390753|gb|CI610979.1|CI610979
EST:     CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGG                         CCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: CCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
EST: gi|88351793|gb|CI624598.1|CI624598
EST:     AACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGG                         CCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC
genomic: AACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGAC

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: 33 (upstream exon), 43 (downstream exon)
Score: 1

TGGTAGGGAGGATTGCGGGATGGAGGCCAGCGCCGGGCTGGTCGCCGGCTCCCACAACCGGAACGAGCTCGTCGTCATCCGCCGCGACGGGGAGCCCGGGgtacgcgcgc ... gtttgtgcagCCGAAGCCGGTGAAGCATACGAATGGGCAGGTGTGCCAGATTTGCGGCGACGACGTCGGCCTCACCCCCGACGGCGAGCCCTTCGTCGCCTGCAACGAGT




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