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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatttaattttgcttgcattgacaattgaaccaaagaaaaggaacaaattttgaaccaaaaggaatacaactttctatgcagcagcttgtgatccagtatagtgcctcctcatattgattgcaaaatacaccttttgcctttctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g42750.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 16
gtagatttaattttgcttgcattgacaattgaaccaaagaaaaggaacaaattttgaaccaaaaggaatacaactttctatgcagcagcttgtgatccagtatagtgcctcctcatattgattgcaaaatacacc--ttttgcctttctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG
                                                 |||| || |          |     |||  |||  |||  || |  | |||||| |    | |  |  |   |     | |  |    |||  || || | ||  ||||||||||||||||||| || |||||||| || || ||||| |||||||||||||| |||||||||||||||||||| || ||||| || || |||||||
-------------------------------------------------aattgtgcattct------tctgttttttcatgt-gcacattattgtgcagtattgcagttgccaacttccttcagtgactgaaatgttttcccccttgtattccagGAAGACTTCTATGCGGTCGTAGATTGGGCTTATAAAATTGACCCCTTGCGTTGCATCTCAATGCATGGGATTACAGAGCGTTACCTTTCTGGACAGAAAG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 16
gtagatttaattttgcttgcattgacaattgaaccaaagaaaaggaacaaattttgaaccaaaaggaatacaactttctatgcagcagcttgtgatccagtatagtgcctcctcatattgattgcaaaatacaccttttgcctttctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG
                                         |  ||   | |  || |   ||||| ||   | | ||  ||||  |       ||||| ||   |   ||  ||| |  ||    ||||   | || |    ||     | |||||||||||||||| ||||| |||||||| ||||||||||| || || || || || |||||||| || || |||||||| || || || ||||||||||
-----------------------------------------atagattgagtcatgta--gaaaggcatggtaatctccctgcataaa-----aatcca-taagatttttcagcatttacatctacaaatctgctttatatgatt-----tcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGCTGTATATCAATGCACGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 16
gtagatttaattttgcttgcattgacaattgaaccaaagaaaaggaacaaattttgaaccaaaaggaatacaactttctatgcagcagcttgtgatccagtatagtgcctcctcatattgattgcaaaatacaccttttgcc-tttctct---tttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG
                                                                  |||   ||  | | |   |    |   |||  | | | ||   |    | |||   ||| | | |     |||    |||||||   || |||||||||||  ||| ||||| ||||||||| |||| |||||||| ||  | ||||| ||||||||||| | ||||||||| || || || ||||||||||
----------------------------------------------------------ttccttataatttgacaatttgtaacgagtttccagatggattttggtatgttaatagatttgctgctataaagttgctttataatttctctgatttcagGAAGACTTCGCTGCTGTTGTGGATTGGGCACACAAAATTGATCCTTTATGCTGCATATCAATGCATGGAACTACAGAACGCTATCTCTCTGGTCAGAAAG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 16
gtagatttaattttgcttgcattgacaattgaaccaaagaaaaggaacaaattttgaaccaaaaggaatacaactttctatgcagcagcttgtgatccagtatagtgcctcctcatattgattgcaaaatacaccttttgcctttctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG
                                                     ||      ||  |   |    ||  | ||  |  |   | |||  |||||| |      ||  |    || ||     ||   |      |    ||| |||||||||||||||| ||||| ||||||||||| |||||||| || || || || || ||||||||||| || |||||||| || || || ||||||||||
-----------------------------------------------------ttccttataattggtcaggttttgttgtgttgttggcagcgatttagtatatttaaaaatc-cagcatttacagctaccaaactgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCATATAAGATTGACCCTTTACGCTGTATATCAATGCATGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 16
gtagatttaattttgcttgcattgacaattgaaccaaagaaaaggaacaaattttgaaccaaaaggaata-caactttctatgcagcagcttgtgatccagtatagtgcctcctcatattgatt-gcaaaatacaccttttgcctttctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG
                                                       ||  |  | |  ||      || | | |    | ||    |   | |  |     |||   | |||| | || ||||    | |||    |    || ||||||||||| ||||| || || ||||||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| ||  | || ||||||||||
-------------------------------------------------------gactcttatgctatggtggtttaccaagtta-atctccaaagtaactccaaaaattccaagttttgactagcgaaatttgtcattttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ29370 (Selaginella moellendorffii), 3'ss of exon 16
gtagatttaattttgcttgcattgacaattgaaccaaagaaaaggaacaaattttgaaccaaaaggaatacaactttctatgcagcagcttgtgatccagtatagtgcctcctcatattgattgcaaaatacaccttttgcctttctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG
                                                                                                      ||| | ||       ||  |||      ||  ||    |  | || ||| |||| || |||||||| ||||| |||||||| |||||  ||||||| ||| | ||||| |||||||| ||||  ||||||||||| || ||  |||| ||||
-----------------------------------------------------------------------------------------------------gtagcgtctatgtgatttcgttg------acgtctaacacaat-ctgtttcagGAGGATTTCTATGCTGTTGTGGATTGGGCTTACAAAGTTGATCCTTTGAGGTGCATCTCAATGCAAGGGACAACAGAACGATATCTCTCAAGTCACAAAG

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|66921504|gb|CX108352.1|CX108352
EST:     AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAG                         GAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT
genomic: AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAGgtagatttaa ... tctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT
EST: gi|58665096|gb|CK053782.1|CK053782
EST:     AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAG                         GAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT
genomic: AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAGgtagatttaa ... tctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT
EST: gi|29645303|gb|CB650310.1|CB650310
EST:     AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAG                         GAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT
genomic: AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAGgtagatttaa ... tctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT
EST: gi|58654154|gb|CK042834.1|CK042834
EST:     AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAG                         GAAGACTTCTATGCGGTTGTCGATTGGGCA
genomic: AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAGgtagatttaa ... tctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCA
EST: gi|58602109|gb|CK012637.1|CK012637
EST:     AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAG                         GAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT
genomic: AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAGgtagatttaa ... tctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT
EST: gi|58612470|gb|CK040182.1|CK040182
EST:     AATCGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAG                         GAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT
genomic: AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAGgtagatttaa ... tctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT
EST: gi|58604329|gb|CK014857.1|CK014857
EST:     AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAG                         GAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT
genomic: AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAGgtagatttaa ... tctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT
EST: gi|29627167|gb|CB632178.1|CB632178
EST:     AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAG                         GAAGACTTCTCCGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT
genomic: AATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAGgtagatttaa ... tctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatagtgcctcctcatattgattgcaaaatacaccttttgcctttctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG
                tattgat  putative branch site (score: 3)
                              tacaccttttgccttt  putative PPT
               atattgatt  TA-rich tract