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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttgtaaacaatgttcagtgcgttggatttaaaataagaatattccatcattttttttctatattctcctagtgccttttcttttgatctttccattttgtttgcaagagacaagAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG

Basic information

species Oryza sativa
transcript LOC_Os04g41100.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G179097_T01 (Zea mays), 3'ss of exon 8
gtacgttgtaaacaatgttcagtgcgttggatttaaaataagaatattccatcattttttttctatattctcctagtgccttttcttttgatctttccattttgtttgcaagagacaagAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG
                       |  ||  ||||||||  | |      ||| |||  |||||| ||| ||||| ||||||||||||||||||||| | ||||||||||||||||||| ||||||| ||||||||||||||||||||||| || |||||||||||||| || |||||||||||  |||
---------------------tggatttaaatttaaaacgaaacatcatcattattagttttctttatgctccttgtgccttttcttttgatctttgcgttttgtttgcaagagacaaaagAAGCGCAGGGGAAGGATGCCTTTTGCTTT-CATCAGGAAATCAATGG-CATTAATACAACTTAGAAG
















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|29623101|gb|CB628112.1|CB628112
EST:     TAACAGCAGTTTCACCTTTGGAACTTCTGTATGTAAAATATTCCAGATTG                         AGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGAC
genomic: TAACAGCAGTTTCACCTTTGGAACTTCTGTATGTAAAATATTCCAGATTGgtacgttgta ... aagagacaagAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattctcctagtgccttttcttttgatctttccattttgtttgcaagagacaagAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG
                     ttttgat  putative branch site (score: 4)
                ttttctttt  TA-rich tract