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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACTACTGGCGCCTCCCCGCCGGCGCCACGCTCAAGGACGTCGTCGTCGTCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCGgtacgtgcgtgtgaattcctaagtttgctgtgggctttgtgtacggcttgtgatgactggattgttcttttgcttgtgatgtgcatgcag

Basic information

species Oryza sativa
transcript LOC_Os02g47200.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47200.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AC233960.1_FGT002 (Zea mays), 5'ss of exon 3
CGACTACTGGCGCCTCCCCGCCGGCGCCACGCTCAAGGACGTCGTCGTCGTCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCGgtacgtgcgtgtgaattcctaagttt---gctgtgggctttgtgtacggcttgtgatgactggattgttcttttgcttgtgatgtgcatgcag----------
|||||||||||  ||||| || |  || ||||||||||| || || ||||| || ||| |||||||||| ||||||||||||||||| ||||| ||||||||| || |   |   ||   |||| |      || | || | |  ||| | | |  | | ||     |  ||       | || |  | |||           
CGACTACTGGCAGCTCCCAGCTGATGCGACGCTCAAGGATGTGGTTGTCGTGGTGCGCTCCGACGAGGCGCACCACCGCGACGTCAATCACTTTGCGTCGgtatgtccac-tcccttggcaagtatcaaatcgtagactgtttaaacgacgtat--taaatgccccctcattcccaaaataatataaacgcatgtcttgtttt

upper sequence: LOC_Os02g47200.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ27318 (Selaginella moellendorffii), 5'ss of exon 3
CGACTACTGGCGCCTCCCCGCCGGCGCCACGCTCAAGGACGTCGTCGTCGTCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCGgtacgtgcgtgtgaattcctaagtttgctgtgggctttgtgtacggcttg-tgatgactggattgttcttttgcttgtgatgtgcatgcag
|||||||||| | || ||    | ||||| | ||   ||||| |||   || ||||||||||||||||| |||||||| ||||| |||||||||||  ||||| |       | || |   |    |   ||||  || |     | ||| | | | |  |                              
CGACTACTGGAGGCTGCCAAAGGACGCCAAGATCCGCGACGTTGTCCAAGTTGTCCGCGCCGACGAGGCTCACCACCGGGACGTGAACCACTTCGCAGCGgtaagc---ctcggatgcaagaagaagggatgggaattctaacgagtttgctcacgcccag------------------------------

upper sequence: LOC_Os02g47200.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ35306 (Selaginella moellendorffii), 5'ss of exon 3
CGACTACTGGCGCCTCCCCGCCGGCGCCACGCTCAAGGACGTCGTCGTCGTCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCGgtacgtgcgtgtgaattcctaagtttgctgtgggctttgtgtacggcttg-tgatgactggattgttcttttgcttgtgatgtgcatgcag
|||||||||| | || ||    | ||||| | ||   ||||| |||   || ||||||||||||||||| |||||||| ||||| |||||||||||  ||||| |       | || |  ||    |   ||||  || |     | ||| | | |    |                              
CGACTACTGGAGGCTGCCAAAGGACGCCAAGATCCGCGACGTTGTCCAAGTTGTCCGCGCCGACGAGGCTCACCACCGGGACGTGAACCACTTCGCAGCGgtaagc---ctcggatgcaaaaagaagggatgggagttctaacgagtttgctcacgcgcag------------------------------

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|86497367|gb|CI140000.1|CI140000
EST:     CCACCGCGACGTCAACCACTTCGCGTCG                         GATGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCCTGCCCCGCTCGA
genomic: CCACCGCGACGTCAACCACTTCGCGTCGgtacgtgcgt ... gtgcatgcagGATGTTCATTTTCAGGGGATGGATCTCAAGGATAT-CCCTGCCCCGCTCGA
EST: gi|87033195|gb|CI187819.1|CI187819
EST:     TCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCG                         GATGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCTGCCCCGCTCGAT
genomic: TCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCGgtacgtgcgt ... gtgcatgcagGATGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCTGCCCCGCTCGAT
EST: gi|87021714|gb|CI276113.1|CI276113
EST:     TCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCG                         GATGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCTGCCCCGCTCGAT
genomic: TCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCGgtacgtgcgt ... gtgcatgcagGATGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCTGCCCCGCTCGAT
EST: gi|88200569|gb|CI200419.1|CI200419
EST:     TCGTCCGCACCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCG                         GATGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCTGCCCCGCTCGAT
genomic: TCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCGgtacgtgcgt ... gtgcatgcagGATGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCTGCCCCGCTCGAT
EST: gi|86492517|gb|CI135150.1|CI135150
EST:     TCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCG                         GAAGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCTGCCCCGCTCGAT
genomic: TCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCGgtacgtgcgt ... gtgcatgcagGATGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCTGCCCCGCTCGAT
EST: gi|88524397|gb|CI452306.1|CI452306
EST:     TCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCG                         GATGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCTGCCCCGCTCGAT
genomic: TCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCGgtacgtgcgt ... gtgcatgcagGATGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCTGCCCCGCTCGAT
EST: gi|218487014|gb|FG958885.1|FG958885
EST:     TCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCG                         GATGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCTGCCCCGCTCGAT
genomic: TCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCGgtacgtgcgt ... gtgcatgcagGATGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCTGCCCCGCTCGAT

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: 70 (upstream exon), 73 (downstream exon)
Score: 5

CGACTACTGGCGCCTCCCCGCCGGCGCCACGCTCAAGGACGTCGTCGTCGTCGTCCGCGCCGACGAGGCACACCACCGCGACGTCAACCACTTCGCGTCGgtacgtgcgt ... gtgcatgcagGATGTTCATTTTCAGGGGATGGATCTCAAGGATATCCCTGCCCCGCTCGATTATCACTGAAGAAATCTTACGGCGGCTTGTGTCCTGCTCAGCTCTGCAG




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