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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattgatgtcgcacgcatgtgcagtgttgatctagctgcttacgaacaatccaacttgatagtcttttctggtagtctgataagggcgttaattggcagGTTTCTCGATCTAGTTCTATTCCTCCAAACACAAGAGATGCATTATACCAAAGTTTGCCACCGACTGTAAAATCGTCCTTGCGTTCTAAGGTGAATTCAT

Basic information

species Oryza sativa
transcript LOC_Os01g65330.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G046846_T01 (Zea mays), 3'ss of exon 9
-----------------------------------------------------------------------------------gaattgatgtcgca--cgcatgtgcagtgttgatctagctgcttacg---aacaatccaacttgatagt--cttttctggtagtctgataagggc--gttaattggcagGTTTCTCGATCTAGTTCTATTCCTCCAAACACAAGAGATGCATTATACCAAAGTTTGCCACCGACTGTAAAATCGTCCTTGCGTTCTAAGGTGAATTCAT
                                                                                   |  |||   | | |      |||||       ||  |  |  ||  |   |  ||  ||  ||  | ||  |||||||||||| || | |||||    | ||||| ||||||||||| || || ||| |||||||||| ||||| |||||||||||||||||||||||||| ||  |||| || ||  | ||||||||| |  | || |
gtaagttcacaggatccactgttctattgttttctctgtgtcctgcattatgcaaatatcatcagtttgacctacagttcatggggttgtactagtagttttgtgtgccacacaaattgaatttgttgtgctaagaaaatcattttttttgtttcttttctggtagcctaacaagggttgatcaattgacagGTTTCTCGTTCAAGCTCTGTTCCTCCAAATACAAGGGATGCATTATACCAAAGTTTGCCACCAACCATAAAGTCATCTCTCCGTTCTAAGCTACACTCCT

upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G148773_T01 (Zea mays), 3'ss of exon 8
gaattgatgtcgcacgcatgtgcagtgttgatctagctgcttacgaacaatccaacttgatagtct--tttctggtagtctgataagggc--gttaattggcagGTTTCTCGATCTAGTTCTATTCCTCCAAACACAAGAGATGCATTATACCAAAGTTTGCCACCGACTGTAAAATCGTCCTTGCGTTCTAAGGTGAATTCAT
    |  | |     |           ||||  | | || ||   |  ||  ||| ||  | |  |  |||||||||| || | |||||    | || || |||||||||||  | || ||  ||||| |||| ||||| ||| |||||||||||||||||||||| ||  |||| || ||  | ||||||||| |  | || |
---ctagtatttggtgtgccacacaaattgaatttgttg-ttctaagaaactcaatttttttgcttattttctggtaggctaacaagggttgatcaaatgacagGTTTCTCGTGCAAGCTCCGTTCCTTCAAATACAAGGGATACATTATACCAAAGTTTGCCACCAACCATAAAGTCATCTCTCCGTTCTAAGCTACACTCCT
















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|29680203|gb|CB676478.1|CB676478
EST:     CAGGCCTTGCACTGCATTACGCCAATATCATCAGTCAGATCGATACTCTT                         GTTTCTCGATCTAGTTCTATTCCTCCAAACACAAGAGATGCATTATACCAA
genomic: CAGGCCTTGCACTGCATTACGCCAATATCATCAGTCAGATCGATACTCTTgtaagctcag ... taattggcagGTTTCTCGATCTAGTTCTATTCCTCCAAACACAAGAGATGCATTATACCAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaatccaacttgatagtcttttctggtagtctgataagggcgttaattggcagGTTTCTCGATCTAGTTCTATTCCTCCAAACACAAGAGATGCATTATACCAAAGTTTGCCACCGACTGTAAAATCGTCCTTGCGTTCTAAGGTGAATTCAT
                                          cgttaat  putative branch site (score: 4)
                                            ttaatt  TA-rich tract