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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgccttagttcaactataattatttctggaactaattgttttttaaattgttcttggaaattgcatttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtatttgctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGATGCAGTGGTGCTCGAATTTTGGTCACCCTGCTTGGT

Basic information

species Oryza sativa
transcript LOC_Os09g07830.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07830.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 12
gtaagc--tgccttagttcaactataattatttctggaactaattgttttttaaattgttcttggaaattgcat-ttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtatttgctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGATGCAGTGGTGCTCGAATTTTGGTCACCCTGCTTGGT
|||||     |||   || ||||   ||| ||| ||||  | |    ||    |||   | |  |||| | ||| ||   |    ||   ||||||  || |    ||||  | || |      || |||    ||||||  ||  ||     ||    | || ||    || ||||||| |||||||| |||||||||||||| || |||||||||||||| || |||||||||||||| |||||||| |||||  |||||
gtaagtgtcacctgtattaaactgccattctttgtggattttagaagttaaacaatcactttcagaaagtacatattgtctcttttttgttatttgctatgcagcagcaacgtgtaat----tgcattataacagtatta--tctgta-----ctaacagcatatgtgtttgcagGAAAAGATTAATGTTCATGGAGGAGCTGTATCCTTAGGACATCCTCTCGGGTGCAGTGGTGCTCGCATTTTGGTTACCCTTATTGGT

upper sequence: LOC_Os09g07830.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 12
gtaagctgccttagttcaactataattatttctggaactaattgttttttaaattgttcttggaaattgcatttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtatttgctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGATGCAGTGGTGCTCGAATTTTGGTCACCCTGCTTGGT
                                                              |||| || |  |   |||  ||     ||||  || |    |||   |||| |   ||   ||| | |  |        ||   ||||        || ||    || ||||||| |||||||| |||||||||||||||||| |||| ||||||||||| ||||| |||||||| |||||||||||||| ||||||
--------------------------------------------------------------gaaaatgtaccttgattctttt-gtagtttgctatgcatcagcagcatttaata--gcatgataataacat-------tctctgtactaacagcacatgtggggttgcagGAAAAGATTAATGTCCATGGAGGAGCTGTGTCTCTAGGGCATCCTCTTGGGTGCAGCGGTGCTCGCATTTTGGTCACCCTTCTTGGT

upper sequence: LOC_Os09g07830.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 10
gtaagc--tgccttagttcaactataattatttctggaactaattgttttttaaattgttcttggaaattgcatttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtatttgctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGATGCAGTGGTGCTCGAATTTTGGTCACCCTGCTTGGT
|||||      |||   | |||||  ||| ||| ||||  | |    |    | ||   | |   |   ||||||         ||   ||||||  || |    ||||  | || |   ||   | |      || || |  ||  |    ||   ||||| ||  | || ||||||| | |||||| ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||||||               
gtaagtgtcatctttactaaactaccattctttgtggattttaaaagtcaaaacatcactttcata---tgcattcg---ctatttttttatttgctatgcagcagcaacatgtaatc--gcatgaca-----atagtattctctcta----ctaacggtatatgtgcgtgcagGAAAAGACTAATGTTCATGGTGGAGCTGTATCTTTAGGACATCCTCTTGGGTGCAGTGGTGCTCGCATTTTG---------------

upper sequence: LOC_Os09g07830.3 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv00s0531g00050.t01 (Vitis vinifera), 3'ss of exon 11
gtaagctgccttagttcaactataattatttctggaactaattgttttttaaattgttcttggaaattgcatttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtattt-gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGATGCAGTGGTGCTCGAATTTTGGTCACCCTGCTTGGT
|| || |||  ||||||| | ||   || || ||       || ||||||||  | |  |     | |  |  |    |   || |||   | |  || ||   |||| ||   | |  |  |  ||||    |||  | |||  |||  |   || | ||| |    |  |||||||  | ||||| ||||| |||||||| ||||| ||||||||  | || |||||||||||||| || ||||||||  || | || 
gtgag-tgctctagttca-ccatctctacttttg------ttttttttttaacctatagtgacttactatacattgaatttgtttact---tcagttttgc--acaatttt--attttcctgaccattttcagatttctgcctctataagcatgtgctcttttgtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGTTGCAGTGGTGCTCGTATCTTGGTCACATTGTTAGGG

upper sequence: LOC_Os09g07830.3 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 12
gtaagctgccttagttcaactataattatttctggaactaattgttttttaaattgttcttggaaattgcatttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtatttgctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGATGCAGTGGTGCTCGAATTTTGGTCACCCTGCTTGGT
                                         |   || ||||||   | |  |    ||  | |  ||  | | ||     || | | |     ||   | | || |       |||   |   ||  ||    | |||    |    |||||||  || |||||||| ||||||| ||||| || ||||| || || ||||||||||| || |||||||| || ||||| |||||||| ||  | || 
----------------------------------------gtgagttcttaaatctgtgtgtgtgtgtgtgtgtgtgtcacatgca-----tgtactcct----caccttattgtttaatttc-tatcggtaccttgttttacaagtacctaccc--catttgct--tgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG

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|88265504|gb|CI376406.1|CI376406
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTA-GACATCCTCTT-GA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88462858|gb|CI519770.1|CI519770
EST:     CTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: CTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|86536502|gb|CI176708.1|CI176708
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88267020|gb|CI378955.1|CI378955
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88468140|gb|CI517599.1|CI517599
EST:     TTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: TTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88267537|gb|CI379472.1|CI379472
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcccaatatttatgtattagttccttaatactctgctggtatttgctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGATGCAGTGGTGCTCGAATTTTGGTCACCCTGCTTGGT
                       ccttaat  putative branch site (score: 4)
                                          tttgctcct  putative PPT
     aatatttatgtattag  TA-rich tract