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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttacactatgcgcttattttgactggtatctgtttctaacatttgtataagataatactaaacgctcttatgtataataatatactattatgatctcttagGCAAGAGGCTGTGTCCTGGTAGCATCTAGTCCAGAAATTCTTACTCGTGTGAGGAAG

Basic information

species Oryza sativa
transcript LOC_Os03g15780.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15780.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 5
gtatatttacactatgcgcttattttgactggtatctgtttctaacatttgtataagataatactaaacgctcttatgtataataatatactattatga---tct-cttagGCAAGAGGCTGTGTCCTGGTAGCATCTAGTCCAGAAATTCTTACTCGTGTGAGGAAG
              |         |  | |     || |||  |||||| ||||  |     ||| |     || |  | | |||||  ||   | |||   |||  ||||||||||||||||||  |||| || |||||||| ||||||||||| || || || |||
-------------gtatagaagcataaagtacaccctatttg-aacattggtatgtg----cactgatttgcctcagattttataatcaacacctttgactgtctatttagGCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG
















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|38565724|gb|CK085177.1|CK085177
EST:     ATCGAGCTTTACGAATTGTGAACCCAAGTCCATACATGGCATATGTACAG                         GCAAGAGGCTGTGTCCTGGTAGCATCTAGTCCAGAAATTCTTACTCGTGTG
genomic: ATCGAGCTTTACGAATTGTGAACCCAAGTCCATACATGGCATATGTACAGgtatatttac ... gatctcttagGCAAGAGGCTGTGTCCTGGTAGCATCTAGTCCAGAAATTCTTACTCGTGTG
EST: gi|29662735|gb|CB659010.1|CB659010
EST:     ATCGAGCTTTACGAATTGTGAACCCAAGTCCATACATGGCATATGTACAG                         GCAAAAGGCTGTGTCCTGGTAGCATCTAGTCCAGAAATTCTTACTCGTGTG
genomic: ATCGAGCTTTACGAATTGTGAACCCAAGTCCATACATGGCATATGTACAGgtatatttac ... gatctcttagGCAAGAGGCTGTGTCCTGGTAGCATCTAGTCCAGAAATTCTTACTCGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagataatactaaacgctcttatgtataataatatactattatgatctcttagGCAAGAGGCTGTGTCCTGGTAGCATCTAGTCCAGAAATTCTTACTCGTGTGAGGAAG
         tactaaa  putative branch site (score: 1)
                                               tctctt  putative PPT
                   tcttatgtataataat  TA-rich tract