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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaacacattgcattttattaataatttactagtaaaccgcgccttttcacttgaagaaattggttcaacactaactataatacttatctttcttgcagTCAGGTGTATCTGAAGTCATATATTTTGTAGAGAAAAGGATTGACAACTCTGATTATGTTTACGTAGCCTCGCACAAGTTGTTATCAATGGCTGGTGTAA

Basic information

species Oryza sativa
transcript LOC_Os01g55974.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55974.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G13950.1 (Glycine max), 3'ss of exon 7
---acaaacacattgcattttattaataa-tttactagtaaaccgcgccttttcacttgaagaaattggttcaacactaactataatacttatctttcttgcagTCAGGTGTATCTGAAGTCATATATTTTGTAGAGAAAAGGATTGACAA-CTCTGATTATGTTTACGTAGCCTCGCACAAGTTGTTATCAATGGCTGGTGTAA
   | |  || |       | ||| | || |||  ||| || |   |       ||  | | | ||||  |   ||     |||  | ||  ||||||||||||||||| || |||||||| || |||||||| ||||| ||  |  | ||  || |||  ||  || || ||||| |||||| |  | ||| ||||||||||| 
atcatattcaaagcaggactgatttacaaatttggtag-aagctttggtgcactaccagtatatattg--tgggcatct-ttatcttgctattctttcttgcagTCAGGAGTTTCTGAAGTAATTTATTTTGTGGAGAAGAGACTAAAAAAATTCAGATATTGCATATGTTGCCTCTCACAAGCTACTGTCATTGGCTGGTGTA-

upper sequence: LOC_Os01g55974.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv17s0000g01370.t01 (Vitis vinifera), 3'ss of exon 7
acaaacacattgcatttta--ttaataattt--actagtaaaccgcgccttttcacttgaagaaattggttcaacactaac-tataatacttatctttcttgcagTCAGGTGTATCTGAAGTCATATATTTTGTAGAGAAAAGGATTGACAACTCTGATTATGTTTACGTAGCCTCGCACAAGTTGTTATCAATGGCTGGTGTAA
  ||  |  |  |   |||  ||   |||||  | | |||  ||  || || |   || |      |   |||| |  ||  | |   |  ||| |||||||||||||||||| ||||||||||| |||||||| ||||| ||| |  |||||||  |   ||  ||  | ||||| |||||  |  ||||||||||||| ||||
--aagtatttgactccttagattctcaatttttatttgtattccctgctttcttgattaattg--ctatatcaagatcaagatcttgcatctat-tttcttgcagTCAGGTGTCTCTGAAGTCATCTATTTTGTGGAGAAGAGGCTGAACAACTCACAAGTTGCATATATCGCCTCTCACAAACTTCTATCAATGGCTGGCGTAA
















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|88841503|gb|CI005583.1|CI005583
EST:     TGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAG                         TCAGGTGTATCTGAAGTCATATATTTTGTAGAGAAAAGGATTGACAACTCT
genomic: TGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAGgtttgtttct ... tttcttgcagTCAGGTGTATCTGAAGTCATATATTTTGTAGAGAAAAGGATTGACAACTCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcacttgaagaaattggttcaacactaactataatacttatctttcttgcagTCAGGTGTATCTGAAGTCATATATTTTGTAGAGAAAAGGATTGACAACTCTGATTATGTTTACGTAGCCTCGCACAAGTTGTTATCAATGGCTGGTGTAA
                         cactaac  putative branch site (score: 1)
                                     tacttatctttctt  putative PPT
                            taactataatacttat  TA-rich tract