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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_Os03g42750.2
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 71 (upstream exon), 73 (downstream exon)
Score: 21

ATGATACATCTGCTGAATTGGGTACATTGAATGATGCTCTTCAAGAACTACTCGATGGAATCCAGgtagatttaa ... tctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatagtgcctcctcatattgattgcaaaatacaccttttgcctttctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG
                tattgat  putative branch site (score: 21)
                              tacaccttttgccttt  putative PPT
               atattgatt  TA-rich tract