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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtatggtatctccaataggtcatgtttggagaaagtaaaaggtttgtgcattacttctaattattttctctctctgtaattgtgttgtcttctacagAATGTTCACCATGCTGGCCAACCAATGCCTGGTGATGAACAGGAGGATGTTCTTATGACCAGTACCCAAACTAGCATCTTAAATGTCACGTGCCCATTAA

Basic information

species Oryza sativa
transcript LOC_Os05g48880.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g48880.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G022065_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------------------------------------------tta-gtatggtatctccaa-taggtcatgt-ttggagaaagtaaaaggtttgt---gcattacttct--aattattttctctctctgtaa-ttgtgttgtcttctacagAATGTTCACCATGCTGGCCAACCAATGCCTGGTGATGAACAGGAGGATGTTCTTATGACCAGTACCCAAACTAGCATCTTAAATGTCACGTGCCCATTAA
                                                                                          | |  || | |  |   |  ||| | |||  || |  ||  |||| | |||||   |  | | |||   ||   | || | | |  ||   || | || | |||| |||||||||||||||||||| || || ||||||||||| |||||||||||  || | ||||| || || || |  ||||||||||||||||| ||||||||||
gtatgtgtttacagagtagcatgctcatggtcatgtgatgaccattgaggattatgcattgtacctgtgctccgggcattacctagttactcacatacgattacaatagctagattatgaatttggaaacataaatgatttgttttgtgtaatttcgcaaaaggtcttatgttttggtgtcttatttttttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATTGTCATGACTAGCACTCAGATGAGCATCTTAAATGTCACATGCCCATTAA

upper sequence: LOC_Os05g48880.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv19s0014g02100.t01 (Vitis vinifera), 3'ss of exon 4
-ttagtatggtatctccaataggtcatgtttggagaaagtaaaaggtttgtgcattacttctaattattttctctctc-tgtaattgtgttgt-cttctacagAATGTTCACCATGCTGGCCAACCAATGCCTGGTGATGAACAGGAGGATGTTCTTATGACCAGTACCCAAACTAGCATCTTAAATGTCACGTGCCCATTAA
 | | |||  | |    |||||    | | ||  |  |  |  |  ||   | |||  || |   ||  |  | | |  |||  |     | | || || ||||||||||||||||| || || |||||||| |||||||| ||||||||  || | ||||||||||| |||   | | |||| ||| | || ||||||||||
ttcattataatgt---gaatagaatttctctgttgtcaagagtaatttctcgaatttattttttctaaatcttatataatgtgttctcactattctcctgcagAATGTTCACCATGCAGGACAGCCAATGCCAGGTGATGAGCAGGAGGACATTGTAATGACCAGTACACAATGCAACCTCTTGAATATTACTTGCCCATTAA
















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|58595967|gb|CK006495.1|CK006495
EST:     CATCAGTAGAGAACCATCTGCTCATTCGGCAGTTCAGAGAGGCAGTTTGG                         AATGTTCACCATGCTGGCCAACCAATGCCTGGTGATGAACAAGAGGATGTT
genomic: CATCAGTAGAGAACCATCTGCTCATTCGGCAGTTCAGAGAGGCAGTTTGGgtatgttccg ... tcttctacagAATGTTCACCATGCTGGCCAACCAATGCCTGGTGATGAACAGGAGGATGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgcattacttctaattattttctctctctgtaattgtgttgtcttctacagAATGTTCACCATGCTGGCCAACCAATGCCTGGTGATGAACAGGAGGATGTTCTTATGACCAGTACCCAAACTAGCATCTTAAATGTCACGTGCCCATTAA
            ttctaat  putative branch site (score: 2)
                                          ttgtcttct  putative PPT
       attacttctaattatt  TA-rich tract