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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_Os09g07830.1
intron # 12
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|86536502|gb|CI176708.1|CI176708
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88256251|gb|CI358639.1|CI358639
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88267020|gb|CI378955.1|CI378955
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|86867692|gb|CI342669.1|CI342669
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88271010|gb|CI386865.1|CI386865
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88270745|gb|CI386003.1|CI386003
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88462858|gb|CI519770.1|CI519770
EST:     CTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: CTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|27410210|gb|CA923280.1|CA923280
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGT
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGT
EST: gi|88243342|gb|CI244464.1|CI244464
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|86412530|gb|CI066935.1|CI066935
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88468574|gb|CI515056.1|CI515056
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGG-ATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88319137|gb|CI513201.1|CI513201
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTTTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88993566|gb|CI110387.1|CI110387
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88436026|gb|CI516562.1|CI516562
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTGTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|29640958|gb|CB645965.1|CB645965
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|86498219|gb|CI140852.1|CI140852
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88468140|gb|CI517599.1|CI517599
EST:     TTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: TTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|87020189|gb|CI259259.1|CI259259
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88907680|gb|CI091078.1|CI091078
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88265504|gb|CI376406.1|CI376406
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTA-GACATCCTCTT-GA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88830971|gb|CI080395.1|CI080395
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|33683367|gb|CF311606.1|CF311606
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88906443|gb|CI375515.1|CI375515
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88267537|gb|CI379472.1|CI379472
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88839196|gb|CI378120.1|CI378120
EST:     GCTGTTGCACTTCCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|5607308|gb|AU075980.1|AU075980
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|86431389|gb|CI085000.1|CI085000
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|88466571|gb|CI532378.1|CI532378
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|89182185|gb|CI113554.1|CI113554
EST:     GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA                         GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
genomic: GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCAgtaagctgcc ... gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGA
EST: gi|86486603|gb|CI129236.1|CI129236
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