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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattagtatatcgtgctgtattgctagacaccagaatgtgccccctttatgctaaatatcatattgccgccatattttgtttacaatctttctttgcagGAGTCTTTTTATTATGGGTTGTCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAG

Basic information

species Oryza sativa
transcript LOC_Os02g17320.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 2
------aaattagtatat-cgtgctgtattgctagacaccagaatgtgccccctttatgctaaatatcatattgccgcca-tattttgtttacaatctttctttgcagGAGTCTTTTTATTATGGGTTGTCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAG
      | |||    | | | ||||  |||     ||      |||   || |  |||    ||| || |||  |  | |  | |  | ||||||| |||   |||||||||| ||||||||||| ||| | ||||| ||||| || ||||| ||| |||||||||||||||||||||
gcaacgagattgcccttttcatgctagattttc--acgttgccatg---ccaccctatttccaatctcttataactacaagcaatgagattacaattttt---tgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAATTATAACTTTGATCATCCAG

upper sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 3
------------------------------------------aaattagtatatcgtgctgtattgctagacaccagaatgtgccccctttatgctaaat-atcatattgccgccatattttgtttacaatctttc---------------------------tttgcagGAGTCTTTTTATTATGGGTTGTCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAG
                                          ||| ||| ||   || ||| |||| ||| ||||| | | ||||| ||| |||||| || |||| ||||||     |   ||||| || ||| |                            |||||||||||| ||||||||||| ||| | ||||| ||||| |||||||||||||||||||| |||||||||||||
gtttgtgcattactgcttggcctcatcttgtggcatatgtgcaaagtagcatg--gtactgcattggtaggcaccaaactatgccctcttcatgctagattatcacattgccatgtcacactgtttccagtctcttataactacaagcaatgaggttacaatatttgcagGAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTCCATGTTCATGATTATAATTTTGATCATCCAG
















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|286561|gb|D15368.1|D15368
EST:     AAATGATAATCGATCAGCTACGTGATCAGCGTGTAGTTGTTGTTACTCAG                         GAGTCTTTTTATTATGGGTTGNCTGATGAGGAATTGG
genomic: AAATGATAATCGATCAGCTACGTGATCAGCGTGTAGTTGTTGTTACTCAGgtttgtccct ... ttctttgcagGAGTCTTTTTATTATGGGTTGTCTGATGAGGAATTGG
EST: gi|29643325|gb|CB648332.1|CB648332
EST:     AAATGATAATCGATCAGCTACGTGATCAGCGTGTAGTTGTTGTTACTCAG                         GAGTCTTTTTATTATGGGTTGTCTGATGAGGAATTGGTCCATGTTCATGAT
genomic: AAATGATAATCGATCAGCTACGTGATCAGCGTGTAGTTGTTGTTACTCAGgtttgtccct ... ttctttgcagGAGTCTTTTTATTATGGGTTGTCTGATGAGGAATTGGTCCATGTTCATGAT
EST: gi|44678675|gb|CR292109.1|CR292109
EST:     AAATGATAATCGATCAGCTACGTGATCAGCGTGTAGTTGTAGTTGCTCAG                         GAGTCTTTTTATAATGGGTTGTCTGATGAGGAATTGGTCCATGTTCATGAT
genomic: AAATGATAATCGATCAGCTACGTGATCAGCGTGTAGTTGTTGTTACTCAGgtttgtccct ... ttctttgcagGAGTCTTTTTATTATGGGTTGTCTGATGAGGAATTGGTCCATGTTCATGAT
EST: gi|33799739|gb|CF325735.1|CF325735
EST:     AAATGATAATCGATCAGCTACGTGATCAGCGTGTAGTTGTTGTTACTCAG                         GAGTCTTTTTATTATGGGTTGTCTGATGAGGAATTGGTCCATGTTCATGAT
genomic: AAATGATAATCGATCAGCTACGTGATCAGCGTGTAGTTGTTGTTACTCAGgtttgtccct ... ttctttgcagGAGTCTTTTTATTATGGGTTGTCTGATGAGGAATTGGTCCATGTTCATGAT
EST: gi|58591679|gb|CF989987.1|CF989987
EST:     AAATGATAATCGATCAGCTACGTGATCAGCGTGTAGTTGTTGTTACTCAG                         GAGTCTTTTTATTATGGGTTGTCTGATGAGGAATTGGTCCATGTTCATGAT
genomic: AAATGATAATCGATCAGCTACGTGATCAGCGTGTAGTTGTTGTTACTCAGgtttgtccct ... ttctttgcagGAGTCTTTTTATTATGGGTTGTCTGATGAGGAATTGGTCCATGTTCATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttatgctaaatatcatattgccgccatattttgtttacaatctttctttgcagGAGTCTTTTTATTATGGGTTGTCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAG
     tgctaaa  putative branch site (score: 2)
                                          tctttctttgc  putative PPT
                           atattttgtttacaat  TA-rich tract