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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgatgtggcaccttgtgttcaatataaaggagtgtgctccttaattcaatctactcgctctcatctgcaaaccatattttgctctcccatctgtcagGTTGACCAGATGGTAATACATTCAGCATCAGACCCCCGCCCTCGGACAACTCTTTGTGGGGATTATTTTTACAACTACTTCTCTCGTGGTATTGATATCT

Basic information

species Oryza sativa
transcript LOC_Os06g49990.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49990.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G116434_T01 (Zea mays), 3'ss of exon 9
acatgatgtggcaccttgtgttcaatataaaggagtgtgctccttaattcaatctactcgctctcatctgcaaaccatatt----ttgctctcccatct-gtcagGTTGACCAGATGGTAATACATTCAGCATCAGACCCCCGCCCTCGGACAACTCTTTGTGGGGATTATTTTTACAACTACTTCTCTCGTGGTATTGATATCT
      | ||| |        |  | | | |      | |||  |       |     |  ||||  ||| ||| |  | |    ||| |||||||||| |  |||| ||||| ||||| ||||| || ||||||||  || | |||||||| || |||||||| ||||| ||||||||||||||||| ||||| ||||||||||
-----gtttggtaaagatcaatataaaaagaatgacattctctctggaatcgttggtgcattctctgctggaaagctaactatgtttgttctcccatcttgcaagGTGGACCAAATGGTCATACACTCCGCATCAGAAGCCAGGCCTCGGACGACCCTTTGTGGAGATTACTTTTACAACTACTTCTCACGTGGAATTGATATCT

upper sequence: LOC_Os06g49990.3 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv04s0023g02970.t01 (Vitis vinifera), 3'ss of exon 9
---acatgatgtggcaccttgtgttcaatataaag-gagtgtgc-tccttaattcaatctactcgctctcatctgcaaaccat-attttgctctcccatctgtcagGTTGACCAGATGGTAATACATTCAGCATCAGACCCCCGCCCTCGGACAACTCTTTGTGGGGATTATTTTTACAACTACTTCTCTCGTGGTATTGATATCT
   | |   | |   |   |   | |||| |     |||| |   |  || ||   | ||| | | |   ||      |   | ||||||||      |    ||||||||||| |||||||| || || || ||||| || ||||| ||||||||||| ||||| ||||| || ||||| || ||   ||||||| | || ||  
tttaaactttata-tatgcttaatccaatgtcttctgagtatttattatttatgttaccta-ttgatggtattgatggagggtgattttgctt----gtaacacagGTTGACCAAATGGTAATTCACTCTGCCTCAGATCCTCGCCCACGGACAACTCTCTGTGGTGATTACTTCTACAATTATTTTGATCGTGGTTTGGACATAC
















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|33687914|gb|CF316153.1|CF316153
EST:     GACGTGTGGACTGAGTTGGGTCGTCCATGTGGCATCCACCAGAAGCAG                         GTTGACCAGATGGTAATACATTCAGCATCAGACCCCCGCCCTCGGACAACT
genomic: GACGTGTGGACTGAGTTGGGTCGTCCATGTGGCATCCACCAGAAGCAGgtcggttttt ... catctgtcagGTTGACCAGATGGTAATACATTCAGCATCAGACCCCCGCCCTCGGACAACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcaatctactcgctctcatctgcaaaccatattttgctctcccatctgtcagGTTGACCAGATGGTAATACATTCAGCATCAGACCCCCGCCCTCGGACAACTCTTTGTGGGGATTATTTTTACAACTACTTCTCTCGTGGTATTGATATCT
 ccttaat  putative branch site (score: 4)
                                  ttttgctctcccatct  putative PPT
                               atatttt  TA-rich tract