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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttttgatggctccatggtttctttatttgtgtttttgtttatttaacaagtactgtaataatgcttcaatcaaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCCTAGTTACTGGATGCAGACTCTTTTCCGTGAATCTAGCGGTGCTATGTTT

Basic information

species Oryza sativa
transcript LOC_Os12g03470.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 14
----------gttagttttga--tggctccatggtttctttatttgt--gtttttgtttatttaacaagtactgtaataatgcttcaatcaaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCCTAGTTACTGGATGCAGACTCTTTTCCGTGAATCTAGCGGTGCTATGTTT
             |  |   |  |     ||||    ||   || ||    | | | ||  | |   |     ||||   || |   || || |||||||||||||||||||||| || || || ||||||||||| || ||||| ||||| ||||||||||||||||| |||||||| || ||||| ||||||||||| 
ccatatatacaccacatacaaattattatcatgcaccctgctttcgttcactctagcttcatcactcatcgtggtaactctgttgggatgaatcaatcagGTGGAACCCAGACGCAATCGTCTTCAACTCCTGGCAGCATTACGGCACTCCCAGTTACTGGATGCAGACGCTTTTCCGCGAGTCTAGTGGTGCTATGTTC

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G393002_T01 (Zea mays), 3'ss of exon 24
gttagttt----tgatggctccatggtttctttatttgtgtttttgtt--tatttaacaagtact--gtaataatgcttcaatcaaacaat-cagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCCTAGTTACTGGATGCAGACTCTTTTCCGTGAATCTAGCGGTGCTATGTTT
|||||| |    | |||||| |    ||   || | | |  |||||||  | || | |  ||| |  |||||  || | |    ||| ||   |||||||||||||||| ||| || || ||| ||||||| || ||||| |||||||| |||||||||||||  |||||||| || || || || || ||| ||
gttagtataaattaatggcttctgctttcacttgtgtttccttttgttcttgttgatctggtattcagtaattgtgttacgggaaaaaaaaatagGTGGAACCCAGACGTCATCGTCTTCAACACCTGGCAGCATTACGGGACTCCTAGCTACTGGATGCAGAAGCTTTTCCGCGAGTCCAGTGGCGCCATGGTT

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
gttagttttgatggctccatggtttctttatttgtgttttt---gtttatttaacaagtactgtaataatgcttcaatcaaac---aatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCCTAGTTACTGGATGCAGACTCTTTTCCGTGAATCTAGCGGTGCTATGTTT
|||||| ||  ||| |   |     || || ||||  ||||   |||  | ||||   | |  | ||  || ||| | ||||     |||||||||||||| ||||| ||||| || |||||||||||||| || ||||||||||| ||||||||||||||  ||||||| || || ||||| || ||| ||
gttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgc-tgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 15
gttagttttgatggctccatggt-ttctttatttgtgttttt---gtttatttaacaagtactgtaataatgcttcaatcaaac---aatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCCTAGTTACTGGATGCAGACTCTTTTCCGTGAATCTAGCGGTGCTATGTTT
|||||| ||  ||| |   |  |   || || ||||  ||||   |||  | ||||   | |  | ||  || ||| | ||||     |||||||||||||| ||||| || || || ||||||||||| || || ||||||||||| ||||||||||||||  ||||||| || || |||||||| ||| | 
gttagtattcttggtttttttttaccctctacttgttcttttcccgttgctctaacgc-tgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGTGCCATGATC

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|29627660|gb|CB632671.1|CB632671
EST:     GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
EST: gi|699908|gb|D46199.1|D46199
EST:     GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
EST: gi|33654398|gb|CF277012.1|CF277012
EST:     GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGNCAACAATACGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
EST: gi|58690391|gb|CK079078.1|CK079078
EST:     GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATATGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
EST: gi|29667818|gb|CB664093.1|CB664093
EST:     GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
EST: gi|29686128|gb|CB682403.1|CB682403
EST:     GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC                         GTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC
genomic: GTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAACgttagttttg ... aaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtttttgtttatttaacaagtactgtaataatgcttcaatcaaacaatcagGTGGAACCCAGACGCCATTGTATTTAACTCCTGGCAACAATACGGAACTCCTAGTTACTGGATGCAGACTCTTTTCCGTGAATCTAGCGGTGCTATGTTT
              atttaac  putative branch site (score: 3)
     tttttgtttatttaac  TA-rich tract