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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacatgctataattcctcactcgtggttgaattgtcaagaatgccttgtccgcacgtcttatggatagttggactaaaccgaactatcgttgtgcagcaaaccagtcagattttttgtgctaatgatgtgttccattgtgtgtttgtgcagCTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAGTAATGAAATGGTTGGGACATATTCAGCCATCCTATTTACCATTGCCAGA

Basic information

species Oryza sativa
transcript LOC_Os02g40090.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G089630_T03 (Zea mays), 3'ss of exon 2
------------------------------------gtaagacatgctataattc-ctcactcgtggttgaattgtcaagaatgccttgtccgcacgtcttatggatagttggactaaaccgaactatcgttgtgcagcaaaccagtcagatt-ttttgtgctaatgatgtgttccattgtgtgtttgtgcagCTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAGTAATGAAATGGTTGGGACATATTCAGCCATCCTATTTACCATTGCCAGA
                                    ||| ||  | | ||   |   |||| || |  |   ||       |   ||   |  |   | ||   || |    | ||||    |||||| | ||||||   |||||||| |||  | || | |||||  |||   |   | | || ||   |||||||||| ||||| ||| | ||||| || |  || ||||||||||||||||||||||||||| ||||| |||||||||| |||||| |||| || || ||
gtaagaccgtgcccaacctttcgttcctataaccgcgtacga-gtacgatgcctaattcacccgcgtctttgtttctgtctaaaactaaactacg-attttgctgagaaccagtctaa-ttaaactatggctgtgcatagaaccagtctgatcgtcttatactaatt-tgttcgctgctatttgcttcgacagCTACAACGTTGACCGGACTTCATTTCGCGATGACGACCTTGATGACATTAGTAATGAAATGGCTGGGATATATTCAGCCGTCCTATCTACCGTTACCTGA

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 1
gtaaga-catgctataattcctcactcgtggttgaattgtcaagaatgccttgtccgcacgtcttatggatagttggactaaaccgaactatcgttgtgcagcaaa--ccagtcagatt-ttttgtgctaatgatgtgttccattgtgtgtttgtgcagCTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAGTAATGAAATGGTTGGGACATATTCAGCCATCCTATTTACCATTGCCAGA
|||||| |||||   |  || ||| || |   || ||        ||||||  | | | || |   |   |   |     |||   |||||   |||||||| |||   ||||| | || | ||||||||||  |||   | |   | || |  | ||||||||||| |||||||| | ||||||||||  |||||||||||||| ||||||||||||||| ||||| ||||||||||||| ||||||||||| |||||
gtaagagcatgcccaa--tcttcattcctaactgcat-----gcgatgcctgattcacgcg-cgccttcttttctatctaaaagtaaactactattgtgcagaaaaattcagtctgcttgtcttgtgctaatt-tgttcactaccttttgctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAGTAATGAAATGGCTGGGATATATTCAGCCATCTTATTTACCATTACCAGA

upper sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv18s0072g00080.t01 (Vitis vinifera), 3'ss of exon 1
gtaagacatgctataattcctcactcgtggttgaattgtcaagaatgccttgtccgcacgtcttatggatagttggactaaaccgaactatcgttgtgcagcaaaccagtcagattttttgtgctaatgatgtgttccattgtgtgtttgtgcagCTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAGTAATGAAATGGTTGGGACATATTCAGCCATCCTATTTACCATTGCCAGA
                                         ||||||  |  | |        |||  |||  |  | |         || |  |  |||  |  |   |||  || |||||  | |  || |     | | |   ||| ||||||||||||||| ||||| ||||||||||  |||||||||||||||||     |  | |  ||| | ||| | || || || ||  || | ||  | |||||
-----------------------------------------agaatgtttatttc----aatatatatatatatatattgg-------tagcaataagcatgatgctcatcat-ttgtttgttttga--attttaattactttaattttttgcagCTACAACATTAACTGGCTTGCATTTTGTTACCACAACCTTGATGACGGCTATTCTTAGGTGGCTTGGATACATCCAACCCTCTCATCTCCCCCTTCCAGA

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|29639689|gb|CB644698.1|CB644698
EST:     TATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTG                         CTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAG
genomic: TATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTGgtaagacatg ... gtttgtgcagCTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAG
EST: gi|88398814|gb|CI601150.1|CI601150
EST:     TATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTATTTTTG                         CTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAG
genomic: TATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTGgtaagacatg ... gtttgtgcagCTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaaccagtcagattttttgtgctaatgatgtgttccattgtgtgtttgtgcagCTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAGTAATGAAATGGTTGGGACATATTCAGCCATCCTATTTACCATTGCCAGA
                     tgctaat  putative branch site (score: 2)
           agatttttt  TA-rich tract