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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcgctgttcgatccgatccgcctccgatccaaaagttcccctcctttgttcttttttttgcgcgattttgcctttttaatcttcgtgtacttactcgattcgattcgattcggtttgtattgctttgctgcagGCGATGGCAGAGGAGGCGAGGGCGCGGTACGAGAAGGCGGTGTTCAAAGTTGTGGATCTG

Basic information

species Oryza sativa
transcript LOC_Os04g55960.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G104294_T01 (Zea mays), 3'ss of exon 1
gtcgctgttcgatccgatccgcctccgatccaaaagttcccctcctttgttcttttttttgcgcgattttgcctttttaatcttcgtgtacttactcgattcgattcgattcggtttgtattgctttgctgcagGCGATGGCAGAGGAGGCGAGGGCGCGGTACGAGAAGGCGGTGTTCAAAGTTGTGGATCTG
                 ||     ||||||| |   | || | ||   |||   | |  | | | | ||||     ||    ||       ||  | |||||||| || ||  |||   ||          ||| ||||||| || |||||||||| ||||||||||||||| ||||| ||||| |||||||||
----------------gtcactgcccgatccga---tcccacacccgcgtttagtctagtactctagtttgttccgttgccttt------tttttttgattcgatgcgtttatgttctcat----------cagTCGATGGCGGACGAGGCGAGGGTGCGGTACGAGAAGGCCGTGTTTAAAGTGGTGGATCTG

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G086489_T02 (Zea mays), 3'ss of exon 1
gtcgctgttcgatccgatccgcctccgatccaaaagttcccctcctttgttcttttttttgcgcgattttgcctttttaatcttcgtgtacttactcgattcgattcgattcggtttgtattgctttgctgcagGCGATGGCAGAGGAGGCGAGGGCGCGGTACGAGAAGGCGGTGTTCAAAGTTGTGGATCTG
                                       | || |    | |  |      |||| ||   |   |||  ||        |||  |   || || ||||| || ||| | |     |    ||| | ||||| ||||||||||||||||||||||||||||| ||||||||||| |||||||||
-------------------------------------gtcgctgcccgatccgatcccactcgcgtttagtctagtttgttccgttgcctctttttttttttgactcgatgcg-tttatgtactcat----cagTCCATGGCGGAGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTG
















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|58667930|gb|CK056616.1|CK056616
EST:     TCACCGTCTTCTTCGGCACGCAGACCGGCACCGCCGAGGGCTTCGCTAAG                         GCGATGGCAGAGGAGGCGAGGGCGCGGTACGAGAAGGCGGTGTTCAAAGTT
genomic: TCACCGTCTTCTTCGGCACGCAGACCGGCACCGCCGAGGGCTTCGCTAAGgtcgctgttc ... tttgctgcagGCGATGGCAGAGGAGGCGAGGGCGCGGTACGAGAAGGCGGTGTTCAAAGTT
EST: gi|66913401|gb|CX100249.1|CX100249
EST:     TC-CGGTCTTCTTCGGCACGCAGACCGGCACCGCCGAGGGCTTCGCTAAG                         GCGATGGCAGAGGAGGCGAGGGCGCGGTACGAGAAGGCGGTGTTCAAAGTT
genomic: TCACCGTCTTCTTCGGCACGCAGACCGGCACCGCCGAGGGCTTCGCTAAGgtcgctgttc ... tttgctgcagGCGATGGCAGAGGAGGCGAGGGCGCGGTACGAGAAGGCGGTGTTCAAAGTT

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: 54 (upstream exon), 60 (downstream exon)
Score: 12

GCCGGTCAAGATCGAGGCCGACGCCGACGCCGACGACGGCCGGAAGCGCGTCACCGTCTTCTTCGGCACGCAGACCGGCACCGCCGAGGGCTTCGCTAAGgtcgctgttc ... tttgctgcagGCGATGGCAGAGGAGGCGAGGGCGCGGTACGAGAAGGCGGTGTTCAAAGTTGTGGATCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttcgtgtacttactcgattcgattcgattcggtttgtattgctttgctgcagGCGATGGCAGAGGAGGCGAGGGCGCGGTACGAGAAGGCGGTGTTCAAAGTTGTGGATCTG
         tacttac  putative branch site (score: 12)
                                         ttgcttt  putative PPT
                                   tttgtatt  TA-rich tract