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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgaataacttgtgccatcgccatgccatcttttgaaaagtatttttgtgttctattattttctttcttggtactaacattttgcacatgtcgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g68320.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68320.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G059020_T01 (Zea mays), 3'ss of exon 8
gtgcg-aataacttgtgccatcgccatgccat--cttttgaaaagtatttttgtgttctattatttt---ctttcttggtactaacattttgcacatgtcgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG
||||   ||  ||  ||  || |  ||    |   | ||  |  |   | |||| ||  |||  |||   |   | |  |  |||| ||| ||  || | ||||   ||||||||||||| |||||||| || |||||||||||||||||||| |||||| |||| || || || || || || |||||||| ||
gtgcacgatctctgctgttattgttattttctggttcttttattgccatgttgtattgaattgattttgacagcccttctcttaacttttagcttatattgtaatgtagGTAATCATAGGCTCACCTGAACTTAAAGCTAATCATTCCATACAACAAATTGTTGAAGTTATTTCAGACCATGAGAAGTATCCAAG

upper sequence: LOC_Os01g68320.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G362850_T01 (Zea mays), 3'ss of exon 7
gtgcg-aataacttgtgccatcgccatgccat--cttttgaaaagtatttttgtgttctattatttt---ctttcttggtactaacattttgcacatgtcgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG
||||   ||  ||| ||  || |  ||    |   | ||  |  |   | |||| ||  |||  |||   |   | |  |  |||| ||| ||  || | ||||  |||||||||||||| |||||||| || |||||||||||||||||||| |||||| |||| || || || || || || |||||||| ||
gtgcacgatctcttctgttattgttattttctggttcttttattgccatgttgtattgaattgattttgacagcccttctcttaacttttagcttatattgtaatgcagGTAATCATAGGCTCACCTGAACTTAAAGCTAATCATTCCATACAACAAATTGTTGAAGTTATTTCAGATCATGAGAAGTATCCAAG
















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|29636635|gb|CB641644.1|CB641644
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29664446|gb|CB660721.1|CB660721
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29675369|gb|CB671644.1|CB671644
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|33797128|gb|CF324429.1|CF324429
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|88417599|gb|CI581622.1|CI581622
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29645557|gb|CB650564.1|CB650564
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29633338|gb|CB638347.1|CB638347
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29673236|gb|CB669511.1|CB669511
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29644134|gb|CB649141.1|CB649141
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29677571|gb|CB673846.1|CB673846
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29640324|gb|CB645333.1|CB645333
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|218485924|gb|FG959170.1|FG959170
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAC                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29675371|gb|CB671646.1|CB671646
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29638139|gb|CB643148.1|CB643148
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29678103|gb|CB674378.1|CB674378
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAGAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29633337|gb|CB638346.1|CB638346
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29669296|gb|CB665571.1|CB665571
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATA
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATA
EST: gi|29670396|gb|CB666671.1|CB666671
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29679220|gb|CB675495.1|CB675495
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29667787|gb|CB664062.1|CB664062
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttctattattttctttcttggtactaacattttgcacatgtcgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG
       tattattttctttctt  TA-rich tract