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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcttttgaagatgcttatttttattctttgcccttgtgtatatgtcaatgtaaagatgtcgctacttgtataatttaattataccttggccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG

Basic information

species Oryza sativa
transcript LOC_Os02g03580.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03580.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G153144_T01 (Zea mays), 3'ss of exon 11
gtcttttgaagatgcttatttttattctttgcccttgtgtatatgtcaatgta--aagatgtcgctacttgtataatttaattataccttggccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG
  ||  ||    |   ||  | |||   | ||| ||||||  | || | | ||  || || |  |  ||     | | | | | || | |||| || ||||||||||||| || ||||||||||| ||| |||||||||||||| | ||||| ||||| |||||||||||||||||||||
tgctgctgtgtttatataactatataagt-gcctttgtgtgcacgttagtataggaaaatctaaccgct-acgaactgtgactgtatcatggcaatattcagGATGAAAGGGAACTCAAGAAGCAAAAACGGAAGCAGTCTAATAGAGAATCGGCACGCAGATCCCGGCTGCGCAAGCAG

upper sequence: LOC_Os02g03580.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G164848_T01 (Zea mays), 3'ss of exon 9
-------------------gtcttttgaagatgcttatttttattctttgcccttgtgtatatgtcaatgta--aagatgt-cgctacttgt---ataatttaattataccttggcca---ttttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG----------------------
                    |  | || |       |||||   |   |||  |||| |  |   ||||| |  || ||     |||||      | | | |  || || |  |  ||   | ||||||||||||| |||||||||||||||||  |||||||||| ||| | || || || || ||||||||||||||||| |||                      
gtacggtcctaactttaaaattgtatgtaccaaaacattttatgtaagtgcttttgtatgcacaccaatgcatgaaaatacatcctactcaccacagactgtgtttgtatcacgtgcaaattgttcagGATGAAAGGGAGCTCAAGAAGCAGAAGCGGAAGCAGTCCAATAGAGAGTCCGCTCGCAGATCCCGGCTGCGCAAACAGGTGTTGTGCAACCCTCGTGCTG

upper sequence: LOC_Os02g03580.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G019106_T01 (Zea mays), 3'ss of exon 11
-------------------gtcttttgaagatgcttatttttattctttgcccttgtgtatatgtcaatgta---aagatgt-cgctacttgt---ataatttaattataccttggcca---ttttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG
                    |  | || |       |||||   |   |||  |||| |  |   ||||| |   || ||     |||||      | | | |  || || |  |  ||   | ||||||||||||| |||||||||||||||||  |||||||||| ||  | || || || || ||||||||||||||||| |||
gtacagtcctaactttacaattgtatgtaccaaaacattttatgtaagtgcttttgtatgcacaccaatgcaggaaaaatacattctactcaccacagactgtgtttgtatcacgtgcaaattgttcagGATGAAAGGGAGCTCAAGAAGCAGAAGCGGAAGCAGTCAAACAGAGAGTCCGCTCGCAGATCCCGGCTGCGCAAACAG

upper sequence: LOC_Os02g03580.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G387310_T01 (Zea mays), 3'ss of exon 9
-------------------gtcttttgaagatgcttatttttattctttgcccttgtgtatatgtcaatgtaaagatgt---cgctacttgt---ataatttaattataccttggcca---ttttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG----------------------
                    |  | || |       |||||   |   |||  |||| |  |   ||||| |   |  |     |||||      | | | |  || || |  |  ||   | ||||||||||||| |||||||||||||||||  |||||||||| ||| | || || || || ||||||||||||||||| |||                      
gtacggtcctaactttaaaattgtatgtaccaaaacattttatgtaagtgcttttgtatgcacaccaatgcaggaaaatacatcctactcaccacagactgtgtttgtatcacgtgcaaattgttcagGATGAAAGGGAGCTCAAGAAGCAGAAGCGGAAGCAGTCCAATAGAGAGTCCGCTCGCAGATCCCGGCTGCGCAAACAGGTGCTGTGCAACCCTCGTGCTG

upper sequence: LOC_Os02g03580.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G34280.3 (Glycine max), 3'ss of exon 4
gtcttttgaagatgcttatttttattctttgcccttgtgtatatgtcaatg-taaagatgtcgctacttgtataatttaattat-accttggcc-----attttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG----------------------
             | | | |||     |  | | || |   |  || | || | |  |  || |||      || ||||||  | | | |  |      | ||| |||| ||||||||||| || |  || |   |||||||||||||||||||||| ||||| |||||| || | || ||||||                      
-------------gttaactttgtcaatcggactttctcattgcgttattggttattacttcactaaactcttattttaatcttcatcctttctgcttaacttttagGACGAAAGAGAGCTTAAAAGACAAAGGCGGAAGCAGTCTAATCGGGAATCTGCACGCAGATCCAGGTTACGGAAGCAGGTGACAGAGAGTATAACCTTTT

upper sequence: LOC_Os02g03580.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G34280.1 (Glycine max), 3'ss of exon 10
gtcttttgaagatgcttatttttattctttgcccttgtgtatatgtcaatg-taaagatgtcgctacttgtataatttaattat-accttggcc-----attttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG
             | | | |||     |  | | || |   |  || | || | |  |  || |||      || ||||||  | | | |  |      | ||| |||| ||||||||||| || |  || |   |||||||||||||||||||||| ||||| |||||| || | || ||||||
-------------gttaactttgtcaatcggactttctcattgcgttattggttattacttcactaaactcttattttaatcttcatcctttctgcttaacttttagGACGAAAGAGAGCTTAAAAGACAAAGGCGGAAGCAGTCTAATCGGGAATCTGCACGCAGATCCAGGTTACGGAAGCAG

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|89197742|gb|CI013732.1|CI013732
EST:     CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGG                         GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
genomic: CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGGgtacaagtcc ... ccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
EST: gi|88903327|gb|CI088865.1|CI088865
EST:     CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGG                         GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
genomic: CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGGgtacaagtcc ... ccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
EST: gi|113931076|gb|DQ883825.1|DQ883825
EST:     CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGG                         GATGAAAGAGAGCTCAAGAATCAGAAAAGGAAGCAGTCTAATCGGGAATCA
genomic: CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGGgtacaagtcc ... ccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
EST: gi|29670500|gb|CB666775.1|CB666775
EST:     CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGG                         GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
genomic: CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGGgtacaagtcc ... ccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
EST: gi|86497997|gb|CI140630.1|CI140630
EST:     CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGG                         GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
genomic: CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGGgtacaagtcc ... ccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
EST: gi|86505811|gb|CI148444.1|CI148444
EST:     CAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGG                         GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
genomic: CAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGGgtacaagtcc ... ccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
EST: gi|29670501|gb|CB666776.1|CB666776
EST:     CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGG                         GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
genomic: CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGGgtacaagtcc ... ccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
EST: gi|88829448|gb|CI074318.1|CI074318
EST:     AGTTCGAGGAGAGCAATGG                         GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
genomic: AGTTCGAGGAGAGCAATGGgtacaagtcc ... ccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
EST: gi|29665043|gb|CB661318.1|CB661318
EST:     CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGG                         GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
genomic: CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGGgtacaagtcc ... ccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
EST: gi|32948093|gb|BP184665.1|BP184665
EST:     CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGG                         GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
genomic: CTGCAATGCATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGGgtacaagtcc ... ccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
EST: gi|86488210|gb|CI130843.1|CI130843
EST:     CATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGG                         GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
genomic: CATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGGgtacaagtcc ... ccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
EST: gi|86252236|gb|CI055973.1|CI055973
EST:     CATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGG                         GATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA
genomic: CATGGCAAAGCATCGTCTGGTTCAGTTCGAGGAGAGCAATGGgtacaagtcc ... ccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatgtaaagatgtcgctacttgtataatttaattataccttggccattttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG
                            atttaat  putative branch site (score: 4)
                                             ccattttc  putative PPT
                  tacttgtataatttaa  TA-rich tract