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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagccaagttttgaaatttgctccagactgtttatatacactgtcagttttaatttccttatcaaaatctggaactcattatacttcctctgaaccgtagGTCAACAACATTGAGCTTATGAGCAAGGGAATACACCCATGCTTTTGGCGAACACCAACTGACAACGACAAGGGAGGCTTCTACACCAAGCCCTATGTTT

Basic information

species Oryza sativa
transcript LOC_Os01g72340.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g72340.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G032496_T01 (Zea mays), 3'ss of exon 7
--tagccaagttttgaaatttgctccag--actgtttatatacactgtcagttttaatttccttatcaaaatctggaactcattatacttcctctgaaccgtagGTCAACAACATTGAGCTTATGAGCAAGGGAATACACCCATGCTTTTGGCGAACACCAACTGACAACGACAAGGGAGGCTTCTACACCAAGCCCTATGTTT
  |      | ||| ||  |  |   ||  | ||  | || | |  |  ||     |   |||||   |||  |  |||||||  | |||   |  |||   |||||||| || ||||||||||||||||||| |||| |||||||||||||||  ||||||||||||||||||| ||||| |||| ||||||||| ||||  |
cattatgttggtttaaaggtcccaatagtaattggctttacatagagaaaggaaccaaagcctta---aaagttaaaactcatggttcttttgc-aaacaacagGTCAACGACGTTGAGCTTATGAGCAAGGGGATACTCCCATGCTTTTGGCGCGCACCAACTGACAACGACAAAGGAGGTTTCTTCACCAAGCCATATGACT
















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|58596245|gb|CK006773.1|CK006773
EST:     CCTGGCAAATCAAAGTAAACAGTATTTCAGGAACAATCGATAGTTGGAAG                         GTCAACAACATTGAGCTTATGAGCAAGGGAATACAGCCATGCTTTT
genomic: CCTGGCAAATCAAAGTAAACAGTATTTCAGGAACAATCGATAGTTGGAAGgtgagactaa ... tgaaccgtagGTCAACAACATTGAGCTTATGAGCAAGGGAATACACCCATGCTTTT
EST: gi|58681122|gb|CK069809.1|CK069809
EST:     CCTGGCAAATCAAAGTAAACAGTATTTCAGGAACAATCGATAGTTGGAAG                         GTCAACAACATTGAGCTTATGAG
genomic: CCTGGCAAATCAAAGTAAACAGTATTTCAGGAACAATCGATAGTTGGAAGgtgagactaa ... tgaaccgtagGTCAACAACATTGAGCTTATGAG
EST: gi|87012504|gb|CI307252.1|CI307252
EST:     CCTGGCAAATCAAAGTAAACAGTATTTCAGGAACAATCGATAGTTGGAAG                         GTCAACAACATTGAGCTTATGAGCAAGGGAATACACCCATGCTTTTGGCGA
genomic: CCTGGCAAATCAAAGTAAACAGTATTTCAGGAACAATCGATAGTTGGAAGgtgagactaa ... tgaaccgtagGTCAACAACATTGAGCTTATGAGCAAGGGAATACACCCATGCTTTTGGCGA
EST: gi|86905446|gb|CI285409.1|CI285409
EST:     CCTGGCAAATCAAAGTAAACAGTATTTCAGGAACAATCGATAGTTGGAAG                         GTCAACAACATTGAGCTTATG
genomic: CCTGGCAAATCAAAGTAAACAGTATTTCAGGAACAATCGATAGTTGGAAGgtgagactaa ... tgaaccgtagGTCAACAACATTGAGCTTATG
EST: gi|29677247|gb|CB673522.1|CB673522
EST:     CCTGGCAAATCAAAGTAAACAGTATTTCAGGAACAATCGATAGTTGGAAG                         GTCAACAACATTGAGCTTATGAGCAAGGGAATACACCCATGCTTTTGGCGA
genomic: CCTGGCAAATCAAAGTAAACAGTATTTCAGGAACAATCGATAGTTGGAAGgtgagactaa ... tgaaccgtagGTCAACAACATTGAGCTTATGAGCAAGGGAATACACCCATGCTTTTGGCGA
EST: gi|58691715|gb|CK080402.1|CK080402
EST:     CCTGGCAAATCAAAGTAAACAGTATTTCAGGAACAATCGATAGTTGGAAG                         GTCAACAACATTGAGCTTATGAGCAAGGGAATACACCCATGCTTTTGGCGA
genomic: CCTGGCAAATCAAAGTAAACAGTATTTCAGGAACAATCGATAGTTGGAAGgtgagactaa ... tgaaccgtagGTCAACAACATTGAGCTTATGAGCAAGGGAATACACCCATGCTTTTGGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttaatttccttatcaaaatctggaactcattatacttcctctgaaccgtagGTCAACAACATTGAGCTTATGAGCAAGGGAATACACCCATGCTTTTGGCGAACACCAACTGACAACGACAAGGGAGGCTTCTACACCAAGCCCTATGTTT
  ttttaat  putative branch site (score: 3)
                                    tacttcctct  putative PPT
             ttatcaaaat  TA-rich tract