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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctccctggtcccaaatcaccaatcttattcctccttgatatgtgagttgaagctttttttctcagtaactggcgaataacacggatatattgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGCATTGCAGGATTTGATGCCAATGGCATGCTTGTGAAGGGCACTCCGGATT

Basic information

species Oryza sativa
transcript LOC_Os10g28320.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g28320.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G813143_T02 (Zea mays), 3'ss of exon 2
ctccctggtcccaaatcaccaatcttattcctccttgatatgtgagttgaagctttttttctcagtaactggcgaataacacggatatattg-ttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGCATTGCAGGATTTGATGCCAATGGCATGCTTGTGAAGGGCACTCCGGATT---------------------------
                     || |    ||   ||||||    | ||| |   ||| |  | |||| |      ||| ||  ||||| ||| |||  |||||| |||| ||  | |||||||||||||| ||| | |||||||| |  |||||||||||||||||||| | |||||||| ||||||||||||||| ||||                           
-------------------tgatttg--cccattttgatacacaaattgcattatttgtcatgagtatc------atatca-agatattttggttgtacaggcattgaaacattttcctcgtgagaagGTGCAAATTGCCACCAAATGTGGCATTGCAGGATTTGATGCAAGTGGCATGCGTGTGAAGGGCACTCCAGATTATGTTCGAGCTTGTTGTGAAGCAAGCC

upper sequence: LOC_Os10g28320.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G813143_T01 (Zea mays), 3'ss of exon 2
--------ctccctggtcccaaatcaccaatcttattcctccttgatatgtgagttgaagctttttttctcagtaactggcgaataacacggatatattg-ttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGCATTGCAGGATTTGATGCCAATGGCATGCTTGTGAAGGGCACTCCGGATT
             |  |||  || ||   || |    ||   ||||||    | ||| |   ||| |  | |||| |      ||| ||  ||||| ||| |||  |||||| |||| ||  | |||||||||||||| ||| | |||||||| |  |||||||||||||||||||| | |||||||| ||||||||||||||| ||||
ggaaagaaaatagtcatcctcaaccaatgatttg--cccattttgatacacaaattgcattatttgtcatgagtatc------atatca-agatattttggttgtacagGCATTGAAACATTTTCCTCGTGAGAAGGTGCAAATTGCCACCAAATGTGGCATTGCAGGATTTGATGCAAGTGGCATGCGTGTGAAGGGCACTCCAGATT
















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|29661845|gb|CB658120.1|CB658120
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|88570556|gb|CI661929.1|CI661929
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|88330876|gb|CI636888.1|CI636888
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|88288363|gb|CI661568.1|CI661568
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|88740122|gb|CI763630.1|CI763630
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|88765993|gb|CI775083.1|CI775083
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|88313763|gb|CI597394.1|CI597394
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|88314009|gb|CI600011.1|CI600011
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|86885716|gb|CI309843.1|CI309843
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|88358029|gb|CI650765.1|CI650765
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|88570554|gb|CI661927.1|CI661927
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|88570743|gb|CI662116.1|CI662116
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|88332260|gb|CI639287.1|CI639287
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|58667429|gb|CK056115.1|CK056115
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|29687719|gb|CB683994.1|CB683994
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTGCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
EST: gi|88826098|gb|CI776663.1|CI776663
EST:     ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAG                         GCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC
genomic: ACACCTCCGATGCCTACGGCCCGCACACCAACGAAGTCCTTCTGGGGAAGgtaataaaat ... tgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgaagctttttttctcagtaactggcgaataacacggatatattgttgaccagGCACTGAAGCAACTACCTCGTGAGAAGGTACAAGTGGCCACCAAGTTCGGCATTGCAGGATTTGATGCCAATGGCATGCTTGTGAAGGGCACTCCGGATT
                            gaataac  putative branch site (score: 2)
                                       atatattgtt  TA-rich tract