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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatgagctaaatgtccttgccagatatattaatctcttaatgttcttactgtcaaagccgttcctatgttaacattagaaagttctattattctatagGGTACGCTTGATGCAGCAAGACGTGCCTCAGCCTTTGTTCGGGGTGACAATGTTGTTCACAAGTTATTCACAGAACTCGCCTACCGCTACAA

Basic information

species Oryza sativa
transcript LOC_Os05g38580.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38580.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G175875_T01 (Zea mays), 3'ss of exon 3
-----atcatgagctaaatgtccttgccagatatattaatctcttaatgttcttactgtcaaagccgttcctatgttaacattagaaagttctattattctatagGGTACGCTTGATGCAGCAAGACGTGCCTCAGCCTTTGTTCGGGGTGACAATGTTGTTCACAAGTTATTCACAGAACTCGCCTACCGCTACAA----
      | ||  |      ||| |     ||| | ||  |  ||| |||| ||    |   || |  | |  |   | | || | | | |   |  ||| | |||||||| |   ||||||| | ||||||  | |||||||||||||||||  |||| ||||| ||| | ||||| || || |||||||||||||     
cttattttatctggcttgggtcttgttttgat-ttttggtggcttgatgt-ctcgaagc--aaacaatgcagaaacttatatcatatattggcacaatt-tgtagGGTACTCAGCATGCAGCGACACGTGCTGCTGCCTTTGTTCGGGGTGATGATGTCGTTCATAAGCTGTTCACTGATCTGGCCTACCGCTACAGTTAA

upper sequence: LOC_Os05g38580.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G112865_T03 (Zea mays), 3'ss of exon 2
--atcatgagctaaat--gtccttgccagatatattaatctcttaatgttcttactgtcaaagccgttcctatgttaacattagaaagttctattattctatagGGTACGCTTGATGCAGCAAGACGTGCCTCAGCCTTTGTTCGGGGTGACAATGTTGTTCACAAGTTATTCACAGAACTCGCCTACCGCTACAA
  ||  | | ||      |  ||||       | || ||  ||| || | |||   |   || |  | |  |   | | || | | | |   |  ||  | |||||||| |   ||||||||||||||||  | |||||||||||||||||  |||| ||||| ||| |||| || || || ||||  ||||||| 
ttatttttatctggcgtggatcttgttcctatttttgatgacttgatat-cttgaagc--aaacaatgcagaaacttatatcatatattgacacgata-tgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG
















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|27547785|gb|CA766051.2|CA766051
EST:     CGAAGGAGGTGCGGACGAAAGCGGATCAGATGGTGCAGCTCGGCAAAGAG                         GGTACGCTTGATGCAGCAAGACGTGCCCCAGCCTTTGTTCGGGGTGACAAT
genomic: CGAAGGAGGTGCGGACGAAAGCGGATCAGATGGTGCAGCTCGGCAAAGAGgtatacattc ... tattctatagGGTACGCTTGATGCAGCAAGACGTGCCTCAGCCTTTGTTCGGGGTGACAAT
EST: gi|86531078|gb|CI171284.1|CI171284
EST:     ACGAAAGCGGATCAGATGGTGCAGCTCGGCAAAGAG                         GGTACGCTTGATGCAGCAAGACGTGCCTCAGCCTTTGTTCGGGGTGACAAT
genomic: ACGAAAGCGGATCAGATGGTGCAGCTCGGCAAAGAGgtatacattc ... tattctatagGGTACGCTTGATGCAGCAAGACGTGCCTCAGCCTTTGTTCGGGGTGACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttactgtcaaagccgttcctatgttaacattagaaagttctattattctatagGGTACGCTTGATGCAGCAAGACGTGCCTCAGCCTTTGTTCGGGGTGACAATGTTGTTCACAAGTTATTCACAGAACTCGCCTACCGCTACAA
                       tgttaac  putative branch site (score: 2)
                                       ttctatt  putative PPT
                                       ttctattattctata  TA-rich tract