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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgttttgtttgttataaactgttgcatacacattttacttttaggctatttgttggaacttgatacagtaacatagtcttttgtaattcatcttgcagGTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCAATCCGTCCTACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA

Basic information

species Oryza sativa
transcript LOC_Os12g25710.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 4
tctgttttgtttgttataaactgttgcatacacatt-----ttacttttaggctatttgttggaacttgataca-gtaacatagtcttttgtaattcatcttgcagGTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCAATCCGTCCTACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA
   |  |||         ||  ||| |||  |  ||     | | ||  |     |   |||  ||| | |  | | || | ||  |  |   |||| ||||||||||||| ||||| |||||||| || |||||||| |||||||| || || |||||||| || ||||||||||||||||||||||||||||||||||||||||
---gagttgcagacaggcaatagtttcatgaaatttgtttgtcaattgaatatcttccattgctactcgctttatgcaaaaaagagtaat---attcttcttgcagGTAGCTTGGGTTACTAAATCTGGGAAATCTGACCTGGAAGCACCGATTGCAATCCGCCCCACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA

upper sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 5
tctgttttgtttgttataaa--ctgttgcatacacattttacttttaggctatttgttggaacttgatacagtaacatagtcttttgtaattcatcttgcagGTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCAATCCGTCCTACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA
  |||||      | ||        ||  | | | || |||    |    |  ||  |   |  | |   | ||   | ||  | |  | ||  || |  |||| || ||||| || ||||| ||| |||| ||| ||||||  ||||| || || ||||| ||||||||||||||||||||||| || |  || || ||||
attgtttaagaactcatggtgctcatttgacaaaaatgttatgaattattttattaatcctatctcacctaatattttggtaatgttgactttttcct--agGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCTATTCGTCCAACAAGTGAGACTGTCATGTATCCCTATTATTCTAAGTGGA
















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|33794258|gb|CF323019.1|CF323019
EST:     AGAATGTCCTACAGAAGGAGAAAGACCACATTGAGGGCTTTGCACCAGAG                         GTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA
genomic: AGAATGTCCTACAGAAGGAGAAAGACCACATTGAGGGCTTTGCACCAGAGgtgtgtattt ... catcttgcagGTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA
EST: gi|58690340|gb|CK079027.1|CK079027
EST:     AGAATGTCCTACAGAAGGAGAAAGACCACATTGAGGGCTTTGCACCAGAG                         GTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA
genomic: AGAATGTCCTACAGAAGGAGAAAGACCACATTGAGGGCTTTGCACCAGAGgtgtgtattt ... catcttgcagGTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA
EST: gi|88312613|gb|CI587521.1|CI587521
EST:     AGAATGTCCTACAGAAGGAGAAAGACCACATTGATGGCTTTGCACCAGAG                         GTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA
genomic: AGAATGTCCTACAGAAGGAGAAAGACCACATTGAGGGCTTTGCACCAGAGgtgtgtattt ... catcttgcagGTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA
EST: gi|12404672|gb|AU166273.1|AU166273
EST:     AGAATGTCCTACAGAAGGAGAAAGACCACATTGAGGGCTTTGCACCAGAG                         GTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA
genomic: AGAATGTCCTACAGAAGGAGAAAGACCACATTGAGGGCTTTGCACCAGAGgtgtgtattt ... catcttgcagGTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA
EST: gi|58674015|gb|CK062701.1|CK062701
EST:     AGAATGTCCTACAGAAGGAGAAAGACCACATTGAGGGCTTTGCACCAGAG                         GTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA
genomic: AGAATGTCCTACAGAAGGAGAAAGACCACATTGAGGGCTTTGCACCAGAGgtgtgtattt ... catcttgcagGTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA
EST: gi|29635079|gb|CB640088.1|CB640088
EST:     AGAATGTCCTACAGAAGGAGAAAGACCACATTGAGGGCTTTGCACCAAAG                         GTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA
genomic: AGAATGTCCTACAGAAGGAGAAAGACCACATTGAGGGCTTTGCACCAGAGgtgtgtattt ... catcttgcagGTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA
EST: gi|58652586|gb|CK041266.1|CK041266
EST:     AGAATGTCCTACAGAAGGAGAAAGACCACATTGAGGGCTTTGCACCAGAG                         GTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA
genomic: AGAATGTCCTACAGAAGGAGAAAGACCACATTGAGGGCTTTGCACCAGAGgtgtgtattt ... catcttgcagGTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctatttgttggaacttgatacagtaacatagtcttttgtaattcatcttgcagGTAGCATGGGTCACTAAATCAGGAAAATCTGATCTGGAAGCTCCTATCGCAATCCGTCCTACAAGTGAGACTGTCATGTATCCATACTTCTCCAAATGGA
                      cagtaac  putative branch site (score: 2)
                                           ttcatctt  putative PPT
                                   ttttgtaatt  TA-rich tract