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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacacacccacaacttgagaaattcgatgtcagtgtacctgtattttttctatggcgttgtcaataatttattgatcaagcccttctcttttgcaagAATGACTGAACTTGAAGAGGGCACTGGAACTGAAGCATCTGACAGCCAACTACTTGAGAAATTCGATCTCAGTGATTCAGAAGACGCAACGAG

Basic information

species Oryza sativa
transcript LOC_Os06g03676.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g03676.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G078458_T04 (Zea mays), 3'ss of exon 14
gtaacacacccacaacttgagaaat--tcgatgt-cagtgtacc-tgta----ttttttctatggcgttgtcaataatttattgatcaagcccttctcttttgcaagAATGACTGAACTTGAAGAGGGCACTGGAACTGAAGCATCTGACAGCCAACTACTTGAGAAATTCGATCTCAGTGATTCAGAAGACGCAACGAG
|||    | || |  ||||   |    |||||||    || ||| | ||    |  ||  | | || |    || ||   |  |||||   | ||| |||||||||||||| ||||||||||||||||| ||||||| ||||||||||||  | |||| || ||| | ||||||  || | |  ||||||||    ||||
gtattcaatcctcctcttgtttacccgtcgatgtattttggaccatatagccgtccttggtctagcatcacgaacaacccacagatcacaacgttcccttttgcaagAATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAG
















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|86524540|gb|CI164746.1|CI164746
EST:     AGTGGTGATAATGGAGCACTGAGTTTGCTTGTGGATCTTCTTAGAGTCAA                         AATGACTGAACTTGAAGAGGGCACTGGAACTGAAGCATCTGACAGCCAACT
genomic: AGTGGTGATAATGGAGCACTGAGTTTGCTTGTGGATCTTCTTAGAGTCAAgtaacacacc ... cttttgcaagAATGACTGAACTTGAAGAGGGCACTGGAACTGAAGCATCTGACAGCCAACT
EST: gi|27548210|gb|CA766314.2|CA766314
EST:     AGTGGTGATAATGGAGCACTGAGTTTGCTTGTGGATCTTCTTAGAGTCAA                         AATGACTGAACTTGAAGAGGGCACTGGAACTGAAGCATCTGACAGCCAACT
genomic: AGTGGTGATAATGGAGCACTGAGTTTGCTTGTGGATCTTCTTAGAGTCAAgtaacacacc ... cttttgcaagAATGACTGAACTTGAAGAGGGCACTGGAACTGAAGCATCTGACAGCCAACT
EST: gi|86526395|gb|CI166601.1|CI166601
EST:     AGTGGTGATAATGGAGCACTGAGTTTGCTTGTGGATCTTCTTAGAGTCAA                         AATGACTGAACTTGAAGAGGGCACTGGAACTGAAGCATCTGACAGCCAACT
genomic: AGTGGTGATAATGGAGCACTGAGTTTGCTTGTGGATCTTCTTAGAGTCAAgtaacacacc ... cttttgcaagAATGACTGAACTTGAAGAGGGCACTGGAACTGAAGCATCTGACAGCCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttctatggcgttgtcaataatttattgatcaagcccttctcttttgcaagAATGACTGAACTTGAAGAGGGCACTGGAACTGAAGCATCTGACAGCCAACTACTTGAGAAATTCGATCTCAGTGATTCAGAAGACGCAACGAG
                           tattgat  putative branch site (score: 3)
                                      cccttctcttttgc  putative PPT
                    aataatttattgatca  TA-rich tract