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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactctaaaatagcatctatttacatcatcggttacttaagattaataactcactgtatggatttttttttcagGCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACCCTGACTGATACATCAAACAAAATAAAAAAGGGAACACTGGGTGATGCTT

Basic information

species Oryza sativa
transcript LOC_Os12g07110.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------------------------gtgactctaaaatagcatctattta----catcatcggttactta-agattaataactcactgtatggatttttttttcagGCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACCCTGACTGATACATCAAACAAAATAAAAAAGGGAACACTGGGTGATGCTT
                                                                      |   |||| | ||    |  |  ||    |   || ||||  ||| | | |  | | |||   | || |  |  |||| ||||||| || |||||||||||||| || ||||||||||||||||| |||||||||| ||||||||| || ||||||||||||||||| || ||||||||||
gtagctttcaatcggcaacaaaatgggtcaaatctgttcactatattgtattttttgaaagacaagggcaggagctctgacattcatttaagataggaactatattggtttattatataatctttattcatcatttgcaaatactttttagGCACTAATGGCTGCTGTTGGGGCCTCAATAGGATATGGATCACCTTTGACCCTGATTGATACATCCAATAAAATAAAAAAGGGAACTCTAGGTGATGCTT

upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 4
gtgactctaaaatagcatctatttacatcatcggttacttaagattaataactcactgtatggatttttttttcagGCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACCCTGACTG-ATACATCAAACAAAATAAAAAAGGGAACACTGGGTGATGCTT
     ||  | |    ||  || | | |   |  ||||| |   || | |  | | |  |  |            ||     | ||||          |||  || | |  || | || |  |   | |||| |  | | | |   |   |  || | |                  
---gttcctataggatatggatctcctttgacccttactgatacttcaaacatgattaaaaagggacaaagG--GGGATGCTACAGCTCTGAGGCCAACTTTAATGGCAGCTGTACCAGCAAT--TCTTGACCGTGTTCGTGATGGAGTGTTCAAGAAG------------------

upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------gtgactctaaaatagcatctatttacatcatcggttacttaagattaataactcactgtat--ggatttttttttcagGCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACCCTGACTGATACATCAAACAAAATAAAAAAGGGAACACTGGGTGATGCTT
                                                  | || | || | |    | || || | | ||   || |||| | |  ||   |      |     ||  || ||| ||    | || || |||||||| | ||  |||||||||||||| || |||||  | ||||||||||||||||||||||||||||| | || ||| ||| |  
gtatgggtttctacttcagtgaatggattgaataaatatttcagtttaaagggaatttagattgtgttttagtttcttaatt--tttcttatgttggatgttttgacaaactcaaatacttgttttagAATTTGATTGCAGCTGTTGGAGGTTGTATAGGATATGGATCTCCTTTGACTTTAACTGATACATCAAACAAAATAAAAAAGGGGAAACAGGGGGATTCCA

upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 4
---------------------------gtgactctaaaatagcatctatttacatcatcggttacttaagatta----ataactcactgtatggatttttttt-----tcagGCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACCCTGACTGATACATCAAACAAAATAAAAAAGGGAACACTGGGTGATGCTT
                            |  |  ||| ||  | ||||||| |||  ||  ||  |    |||     ||  ||   | |    |  ||   |     | ||    | || || |||||||||| | | |||||||||||||| ||  ||||| | |||||||| |||||||| || ||||| ||||||  ||| |||||| 
gtatgtggatatacttttcttgaataaattccaataatatttcttctatttccattttcttttgttctttattcttttatttcttgttttgacaaacttgcctacatgttagAATTTGATGGCAGCTGTTGGGGTTCCTATAGGATATGGATCTCCTCTGACCTTTACTGATACTTCAAACAAGATTAAAAAAGGAACAAAGGGGGATGCTA

upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 5
-------gtgactctaaaatagcatctatttacatcatcggtt---acttaagattaataactcactgtatggatttttttttcagGCAC-TCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACCCTGACTGATACATCAAACAAAATAAAAAAGGGAACACTGGGTGATGCTT
          | |  |  |    ||   |||| ||    | |    |||| ||| || |      | |  |   |   || ||   |  | | || ||| || |||||  | | || |||||||| || |||||||| || || ||||| |||||||| ||||||||||| |||   || ||||   
gtatcttaaaagttcattactcaatgcgtttatatagcagttccacacttcagagtatttgaatgcggcctaattccattgttgtagAGCGTAATGGCTACTATTGGGAGTGCTATTGGATATGGGTCTCCCTTGACGCTAACGGATACTTCAAACAAGATAAAAAAGGGTACAAAAGGAGATGTCA

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|29614988|gb|CB620001.1|CB620001
EST:     TATACCTGGCCTACCTGCCACTTGCACACATTCTTGAGTTGGCAGCTGAG                         GCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACC
genomic: TATACCTGGCCTACCTGCCACTTGCACACATTCTTGAGTTGGCAGCTGAGgtgactctaa ... tttttttcagGCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACC
EST: gi|29675500|gb|CB671775.1|CB671775
EST:     TATACCTGGCCTACCTGCCACTTGCACACATTCTTGAGTTGGCAGCTGAG                         GCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACC
genomic: TATACCTGGCCTACCTGCCACTTGCACACATTCTTGAGTTGGCAGCTGAGgtgactctaa ... tttttttcagGCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACC
EST: gi|86829547|gb|CI286740.1|CI286740
EST:     TATACCTGGCCTACCTGCCACTTGCACACATTCTTGAGTTGGCAGCTGAG                         GCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACC
genomic: TATACCTGGCCTACCTGCCACTTGCACACATTCTTGAGTTGGCAGCTGAGgtgactctaa ... tttttttcagGCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACC
EST: gi|58030548|gb|CX728091.1|CX728091
EST:     GCCTACCTGCCACTTGCACACATTCTTGAGTTGGCAGCTGAG                         GCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACC
genomic: GCCTACCTGCCACTTGCACACATTCTTGAGTTGGCAGCTGAGgtgactctaa ... tttttttcagGCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACC
EST: gi|29672201|gb|CB668476.1|CB668476
EST:     TATACCTGGCCTACCTGCCACTTGCACACATTCTTGAGTTGGCAGCTGAG                         GCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACC
genomic: TATACCTGGCCTACCTGCCACTTGCACACATTCTTGAGTTGGCAGCTGAGgtgactctaa ... tttttttcagGCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACC
EST: gi|29614945|gb|CB619958.1|CB619958
EST:     TATACCTGGCCTACCTGCCACTTGCACACATTCTTGAGTTGGCAGCTGAG                         GCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACC
genomic: TATACCTGGCCTACCTGCCACTTGCACACATTCTTGAGTTGGCAGCTGAGgtgactctaa ... tttttttcagGCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacatcatcggttacttaagattaataactcactgtatggatttttttttcagGCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACCCTGACTGATACATCAAACAAAATAAAAAAGGGAACACTGGGTGATGCTT
                                           tttttttttc  CT-rich tract
             ttacttaagattaata  TA-rich tract