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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgaatatatcatcactattttctatttgtttagttttaggaagaatataatttgctgttcttgactagcttgccactgattgtctatttgtttagttttaggaagaatataaactgttatttaccaaaacattaatttgttttctttatgctataaatatgaagaaaagattacaaatgttttttttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTGGTCACTTCTGCTGTTATTGCAAAGGTTCACACTATTGATTGGACTGTCG

Basic information

species Oryza sativa
transcript LOC_Os12g26290.6
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 6
lower sequence: AC205471.4_FGT004 (Zea mays), 3'ss of exon 3
gtaagcgaatatatcatcactattttctatttgtttagttt-taggaagaatataatttgctgttcttgactagcttgccactgattgtctatttgtttagttttaggaagaatataaactgttatttaccaaaacattaatttgttttctttatgctataaatatgaagaaaagattacaaatgtttttttta-atctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTGGTCACTTCTGCTGTTATTGCAAAGGTTCACACTATTGATTGGACTGTCG
||||| |||   ||||  | |||| |||||||||||||||| || |||||||     ||| ||||||||| |  ||| |||| |  |  | ||               ||   | |    | ||| ||||||| |||||||     ||| ||||||||| |||||||||||||  |||  ||||||| |||| | ||||||||||||||||||||||||||||||||||||||||||||||||||| | |||||||||||||||||| |||||||||||||||||| |||||||| ||||||
gtaagagaa-gcatcactattattatctatttgtttagtttatatgaagaat-----ttgatgttcttgattt-ctttccaccg--taccgat---------------aaagttgttgtttattaattaccaagacattaa-----tttttttatgcta-aaatatgaagaaacaatttaaaatgttattttgatatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCTAGATTGGTCACTTCTGCTGTCATTGCAAAGGTTCACACTGTTGATTGGGCTGTCG

upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G818450_T01 (Zea mays), 3'ss of exon 1
gtaagcgaatatatcatcactattttctatttgtttagttt-taggaagaatataatttgctgttcttgactagcttgccactgattgtctatttgtttagttttaggaagaatataaactgttatttaccaaaacattaatttgttttctttatgctataaatatgaagaaaagattacaaatgtttttttta-atctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTGGTCACTTCTGCTGTTATTGCAAAGGTTCACACTATTGATTGGACTGTCG
||||| |||   ||||  | |||| |||||||||||||||| || |||||||     ||| ||||||||| |  ||| ||||    |  | ||               ||   | |    | ||| ||||||| |||||||     ||| ||||||||| |||||||||||||  |||| ||||||| |||| | ||||||||||||||||||||||||||||||| ||||||||||||||||||| | |||||||||||||| ||| ||||| |||||||||||| |||||||||||||||
gtaagagaa-gcatcactattattatctatttgtttagtttatatgaagaat-----ttgatgttcttgattt-ctttccacca--taccgat---------------aaagttgttgtttattaattaccaagacattaa-----tttttttatgcta-aaatatgaagaaacaatta-aaatgttcttttaatatctcagGAAGAACATCCCAACCTATCAGACAAAGAATTATATCGGTATGCTAGATTGGTCACTTCTGTTGTCATTGCGAAGGTTCACACTCTTGATTGGACTGTCG

upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G312997_T01 (Zea mays), 3'ss of exon 5
gtaagcgaatatatcatcactattttctatttgtttagttt-taggaagaatataatttgctgttcttgactagcttgccactgattgtctatttgtttagttttaggaagaatataaactgttatttaccaaaacattaatttgttttctttatgctataaatatgaagaaaagattacaaatgttttttttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTGGTCACTTCTGCTGTTATTGCAAAGGTTCACACTATTGATTGGACTGTCG
||||| |||   |||   | |||| ||||||| |||||||| || |||||||     ||| ||||||||| |  ||| |||| |  |  | ||     |  ||||               | ||| ||||||| ||||||||||      ||||||||| |||||||||||||  |||||||||||  |||| |||||||||||||||||||||||||||||||||||||||||||||| ||||| | |||||||||||||||||| |||||||||||||||||||||||||||||||| |
gtaagagaa-gcatcgctattattatctatttatttagtttatatgaagaat-----ttgatgttcttgattt-ctttccaccg--taccgataaagctgttttt---------------tattaattaccaagacattaattt------tttatgcta-aaatatgaagaaacaattacaaatgtcctttt-aatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGATATGCTAGATTGGTCACTTCTGCTGTCATTGCAAAGGTTCACACTATTGATTGGACTGTGG

upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G100724_T01 (Zea mays), 3'ss of exon 3
gtaagcgaa-tat-atcatcactattttctatttgtttagttt-taggaagaatataatttgctgttcttgactagcttgccactgattgtctatttgtttagttttaggaagaatataaactgttatttaccaaaacattaatttgttttctttatgctataaatatgaagaaaagattacaaatgtttttttta-atctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTGGTCACTTCTGCTGTTATTGCAAAGGTTCACACTATTGATTGGACTGTCG
||||| |||  || |  || | |||  |||||||||||||||| || |||||||     ||| ||||||||| |  ||| |||| |  |  | ||               ||   | |    | ||| ||||||| ||||||||||      ||||||||| |||||||||||||  |||| ||||||| |||| | |||||||||||||||| |||||||||||||||||||||||||||||||||||| |||||||||||||| ||| ||||||||||||||||||||||||||||||||||
gtaagagaagcatcactattattatcatctatttgtttagtttatatgaagaat-----ttgatgttcttgattt-ctttccaccg--taccgat---------------aaagctgttgtttattaattaccaagacattaattt------tttatgcta-aaatatgaagaaacaattaaaaatgttcttttaatatctcagGAAGAACATACCAACCTATCAGACGAAGAATTATATCGGTATGCCAGATTGGTCACTTCTGTTGTCATTGCAAAGGTTCACACTATTGATTGGACTGTCG

upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G04410.1 (Glycine max), 3'ss of exon 5
gtaagcgaatatatcatcactattttctatttgtttagttttaggaagaatataatttgctgttcttgactagcttgccactgattgtctatttgtttagttttaggaagaatataaactgttatttaccaaaacattaatttgttttctttatgctataaatatgaagaaaagattacaaatgttttttttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTGGTCACTTCTGCTGTTATTGCAAAGGTTCACACTATTGATTGGACTGTCG
                                                                                              |  |  |   |   | |||  ||    | | |     | | ||  |    |       |  |  ||| | || | |   |  |  |  |   |    | || |||| || |  ||||  || |   ||| |||||| | |||||  |||| | |||||| || || ||||| |||||||||||||| || |||||||||||||| |
----------------------------------------------------------------------------------------------ggctgatccaatataaaattaaagtcataact-----atatatatacgcatgaaaagaaaacactaactgtgtacatctgtctctattttaatgcactcat-tcagAAACATTATCCTCACTTGGGAGATGAAGAACTTTATCGCCATGCTAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACGATTGATTGGACTGTAG

upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G01470.1 (Glycine max), 3'ss of exon 5
gtaagcgaatatatcatcactattttctatttgtttagttttaggaagaatataatttgctgttcttgactagcttgccactgattgtctatttgtttagttttaggaagaatataaactgttatt-taccaaaacattaatttgttttctttatgctataaatatgaagaaaagattacaaatgttttttttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTGGTCACTTCTGCTGTTATTGCAAAGGTTCACACTATTGATTGGACTGTCG
                                                                                                    | | |  |  ||| | | |  ||| | ||   |||||   || |        |||    ||| |||| | |      |  |  |   |    | || |||| || |  ||||  |  |   ||| |||||| | |||||  |||||| |||||| || || ||||| |||||||||||||| || |||||||||||||| |
-------------------------------------------------------------------------------------------------acatatcaaaattaatgtca-caattactatatataaaca--gatgtaaagaaaatatatactaactatgtacatccatctctattttaatgcactcat-tcagAAACATTATCCTCAATTGGGAGATGAAGAACTTTATCGCCATGCCAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAG

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|29673790|gb|CB670065.1|CB670065
EST:     TACAAGCTCTTTTTGTTAAGGAACACAATGCAGTTTGTGATGCAATAAAG                         GAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTG
genomic: TACAAGCTCTTTTTGTTAAGGAACACAATGCAGTTTGTGATGCAATAAAGgtaagcgaat ... ttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTG
EST: gi|29677261|gb|CB673536.1|CB673536
EST:     TACAAGCTCTTTTTGTTAAGGAACACAATGCAGTTTGTGATGCAATAAAG                         GAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTG
genomic: TACAAGCTCTTTTTGTTAAGGAACACAATGCAGTTTGTGATGCAATAAAGgtaagcgaat ... ttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTG
EST: gi|29629207|gb|CB634218.1|CB634218
EST:     TACAAGCTCTTTTTGTTAAGGAACACAATGCAGTTTGTGATGCAATAAAG                         GAAGAACATCCCAACCTATCGGACGAAGAATTGTATCGGTATGCCAAATTG
genomic: TACAAGCTCTTTTTGTTAAGGAACACAATGCAGTTTGTGATGCAATAAAGgtaagcgaat ... ttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTG
EST: gi|25778087|gb|CA752839.1|CA752839
EST:     TACAAGCTCTTTTTGTTAAGGAACACAATGCAGTTTGTGATGCAATAAAG                         GAAGAACATCCCAACCTATCGGACGAAGAATTGTATCGGTATGCCAAAT
genomic: TACAAGCTCTTTTTGTTAAGGAACACAATGCAGTTTGTGATGCAATAAAGgtaagcgaat ... ttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAAT
EST: gi|25778064|gb|CA752816.1|CA752816
EST:     TACAAGCTCTTTTTGTTAAGGAACACAATGCAGTTTGTGATGCAATAAAG                         GAAGA-CATCCCAACCTATCGGACGAAGAATTGTATCGGTATGCCAAATTG
genomic: TACAAGCTCTTTTTGTTAAGGAACACAATGCAGTTTGTGATGCAATAAAGgtaagcgaat ... ttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTG
EST: gi|29627242|gb|CB632253.1|CB632253
EST:     TACAAGCTCTTTTTGTTAAGGAACACAATGCAGTTTGTGATGCAATAAAG                         GAAGAACATCCCAACCTATCGGACGAAGAATTGTATCGGTATGCCCAATTG
genomic: TACAAGCTCTTTTTGTTAAGGAACACAATGCAGTTTGTGATGCAATAAAGgtaagcgaat ... ttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttatgctataaatatgaagaaaagattacaaatgttttttttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTGGTCACTTCTGCTGTTATTGCAAAGGTTCACACTATTGATTGGACTGTCG
                                           ttttaat  putative branch site (score: 3)
                                       ttttttttaatctc  CT-rich tract
           tataaatatgaagaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgaatatatcatcactattttctatttgtttagttttaggaagaatataatttgctgttcttgactagcttgccactgattgtctatttgtttagttttaggaagaatataaactgttatttaccaaaacattaatttgttttctttatgctataaatatgaagaaaagattacaaatgttttttttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTGGTCACTTCTGCTGTTATTGCAAAGGTTCACACTATTGATTGGACTGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG