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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctgttatattggaatgaacttctttcatctgatggaaattcatagtatgttttttttgacgaaatcctcgagcaacttgctaattttttttgtcatggtagtatgttcatacgagtcttcatgtacttttgtcagATAGCACAGGTTCATCGTGCAACTCTTGTAGATGGCAGAGAAGTAGTTGTGAAAATCCAACATGATGGTATCAAAGATATCATATTAGAG

Basic information

species Oryza sativa
transcript LOC_Os06g48770.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g48770.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 5
gtaagttctgttatattggaatgaacttctttcatctgatggaaattcatagtatgttttttttgacgaaatcctcgagcaacttgctaattttttttgtcatggtagtatgttcatacgagtcttcatgtacttttgtcagATAGCACAGGTTCATCGTGCAACTCTTGTAGATGGCAGAGAAGTAGTTGTGAAAATCCAACATGATGGTATCAAAGATATCATATTAGAG
|||||| ||||  ||    | |||||||   | |||||||  |||| ||||||||| |  |||       | |                  |||| || |||       |||  |||  |                |  ||||||||||| ||||||||||||||||| | ||||||||||||||||||||| ||||| || ||||||||| | || || ||||||||||||
gtaagtactgtattagcaaactgaactttacttatctgatataaat-catagtatgctcatttcatatggacc------------------ttttattttca-------atgaacatttgg---------------taacagATAGCACAAGTTCATCGTGCAACTCTGGCAGATGGCAGAGAAGTAGTTGTCAAAATTCAGCATGATGGTGTGAAGGAGATCATATTAGAG
















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|88977704|gb|CI384186.1|CI384186
EST:     TGAATGATCTGTTTGCTAATTTTGTGCTGGATCCTCTAGCAACTGCATCA                         ATAGCACAGGTTCATCGTGCAACTCTTGTAGATGGCAGAGAAGTAGTTGTG
genomic: TGAATGATCTGTTTGCTAATTTTGTGCTGGATCCTCTAGCAACTGCATCAgtaagttctg ... cttttgtcagATAGCACAGGTTCATCGTGCAACTCTTGTAGATGGCAGAGAAGTAGTTGTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattttttttgtcatggtagtatgttcatacgagtcttcatgtacttttgtcagATAGCACAGGTTCATCGTGCAACTCTTGTAGATGGCAGAGAAGTAGTTGTGAAAATCCAACATGATGGTATCAAAGATATCATATTAGAG
 tgctaat  putative branch site (score: 2)
                                             cttttgtc  putative PPT
     ttttttgt  TA-rich tract