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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgacgattggaataagctgatcttccacttttggaatctagaaataagggtacaggtttgtatttgttctttgttaatctttatgagttctctgttcagGAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCGTGATATTGTTGGATTACTTTTAAATGGAATTGATCTTCCTAACTCTAGA

Basic information

species Oryza sativa
transcript LOC_Os08g42740.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42740.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 2
-ttgacgattggaataagctgatcttccacttttgg--aatctagaaataagggtacaggtttgtatttgttctttgttaatctttatgagttctctgttcagGAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCGTGATATTGTTGGATTACTTTTAAATGGAATTGATCTTCCTAACTCTAGA
 |||        ||||  ||||  ||    | ||||   ||   | |  |  |  ||   | |  || || ||| |||   |     ||  |||  | | |||||||||||||||| | || || ||||||||||| |||||||||||||| ||  ||| |||||| |||||||| ||||||| | ||   ||   |||||| 
tttgctagaatcaatacactgacattttcttattggtggatggtgtagaagtgaaactaatgtacatctgctctctgtgtgttc---tgtattcattatgcagGAACATCAGCAAGCTGAGTGACGAATGGTTTGCAGATGAAGAAAAAGTCCGCCATACTGTTGGCTTACTTTTGAATGGAAATCATGACCCCCGCTCTAGG

upper sequence: LOC_Os08g42740.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G143644_T01 (Zea mays), 3'ss of exon 2
--ttgacgattggaataagctgatcttccacttttggaatctagaaataag-ggtacaggtttgtatttgttctttgt-taatctttatgagttctctgttcagGAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCGTGATATTGTTGGATTACTTTTAAATGGAATTGATCTTCCTAACTCTAGA
    |      | |||    || | ||    | |||  |  |||    ||| |  ||   |    || ||| | |||| |  ||| |||    ||  | | |||||||||||||||||| || |||||||||||||| |||||||||||||| ||  ||| |||||| |||||||| ||||||| | ||   ||   |||||| 
ctgcgctagaagcaatgctgtggtattttcttattgctagatagctggaagtgaaactaatgcacatctgtgccttgtgtgttctctat----tcattatgcagGAACATCAGCAAGTTGAGTGATGAATGGTTTGCAGATGAAGAAAAAGTCCGCCATACTGTTGGCTTACTTTTGAATGGAAATCATGAGCCCGGCTCTAGG
















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|58672626|gb|CK061312.1|CK061312
EST:     CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTACAAATG                         GAACATCAGCAAGCTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCG
genomic: CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTACAAATGgtaagtttgt ... ctctgttcagGAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCG
EST: gi|58680866|gb|CK069553.1|CK069553
EST:     CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTACAAATG                         GAACATCAGCAAGCTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCG
genomic: CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTACAAATGgtaagtttgt ... ctctgttcagGAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCG
EST: gi|88312074|gb|CI580239.1|CI580239
EST:     CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTACAAATG                         GAACATCAGCAAGTTAAGCGATGAATGGTTTGGGGATGAAGAAAAAGTTCG
genomic: CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTACAAATGgtaagtttgt ... ctctgttcagGAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCG
EST: gi|29622679|gb|CB627690.1|CB627690
EST:     CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTACAAATG                         GAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCG
genomic: CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTACAAATGgtaagtttgt ... ctctgttcagGAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCG
EST: gi|29671896|gb|CB668171.1|CB668171
EST:     CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTACAAATG                         GAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCG
genomic: CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTACAAATGgtaagtttgt ... ctctgttcagGAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCG
EST: gi|29669832|gb|CB666107.1|CB666107
EST:     CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTACAAATG                         GAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCG
genomic: CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTACAAATGgtaagtttgt ... ctctgttcagGAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCG
EST: gi|33793942|gb|CF322859.1|CF322859
EST:     CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTAC-----                         -AA-AT--GCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCG
genomic: CTATCGATTCGAAGGGAGGAGGCGTGTGTTCTTCTTCATCACTACAAATGgtaagtttgt ... ctctgttcagGAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagggtacaggtttgtatttgttctttgttaatctttatgagttctctgttcagGAACATCAGCAAGTTAAGCGATGAATGGTTTGCGGATGAAGAAAAAGTTCGTGATATTGTTGGATTACTTTTAAATGGAATTGATCTTCCTAACTCTAGA
                           tgttaat  putative branch site (score: 3)
                                           ttctctgttc  putative PPT
                         tttgttaatctttat  TA-rich tract