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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaaccagtccctttctgagaataatatacctccatttcgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g73790.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 5
TGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaaccagtccctttctgagaataatatacct--ccattt---cgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcag
 ||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||| ||||| |||||||||||||| || |||||||||||| ||   |  ||  |||  |||| || ||   | |    ||||   |   ||| ||  | |||||| |||||| | |   ||||||  |||||||
CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcag

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G167872_T02 (Zea mays), 5'ss of exon 3
TGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaaccagtcccttt---------ctgagaataatatacctccattt-cgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcag
 ||||||||||| ||||||||||| ||||| ||||| || ||||||||||| |||||||||||||||||||| || |||||  |||| || |||||||||||||||  ||  ||   |||         ||||| ||  |   | |   ||| |   || | | || |||| | |||||| |||        |         
CGTGAGACCTTTTAATTGGATTGGGCCAAGGATGGATTTCATTCCTGGTGTCGATGGTCCTAGTGAGGGTGTACCCCGGGTGCTGGCTTGCTTCAGTAACgtatgtgcacttgtttttttatttattttctgagtatggttggcttaattttgcaccatag-cattcttctgagaagatgcatggttttgcag---------

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 5
TGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaaccagtcccttt-ctgagaataatatacctccattt-cgttatggtcgtttttctcataagatgt--atgtcgccaatga------atttgcag
||| || || || || |||||||||||  ||||||| || ||||||||  |||||||||| ||||||||||||||||||||| | || || || || || ||  || |   | |     |  ||    |  |  |  |   ||    || | | ||   || | | ||  |||  |  |   |  |         | |||||
TGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGAGGGTGTTCCTCGGGTTCTTGCTTGCTTTAGCAATgtcagttacttacttttgctattgctttttgttgaagtttgttgatattttagccggagttttgaaaatttgttcaaattttctgttttcctttgtctgcag

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA12G30490.2 (Glycine max), 5'ss of exon 5
TGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaaccagtccctttctgagaataatatacctccatttcgttatggtcgtttttctcataagatg--------tatgtcgccaatgaatttgcag---
|||||| ||||| ||||||||||||||| ||||||| || ||||| ||  ||||||| || ||||||||||||||||||||| ||||||| || || || ||  ||  || | |    ||  ||   |  |  | ||    |   |  |  ||| | || |   |  |||        ||| |   | ||   ||| | |   
TGTGAGGCCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGCCCAAGTGAGGGTGTTCCTCGGGTTCTGGCATGCTTTAGCAATgtgagtttac-attttgatttagactttgtttaagcttgtatatatgttactcgatatttttggataatgattctaaatattttctccattccttttctgtag

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA17G05440.1 (Glycine max), 5'ss of exon 3
TGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaaccagtccctttctgagaataatatacctc---catttcgttat-ggtcgtttttctcataagatgtatgtcgccaatgaatttgcag-----------
|||||||||||| ||||||||||||||| ||||||| || ||||| ||  |||||||||| ||||||||||||||||||||| ||||||| || || || ||  ||  || | |    ||  ||   |  |  | ||     || | ||| |  |||  | || | | |  |||  | |    | |   ||                
TGTGAGACCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGTCCAAGTGAGGGTGTTCCTCGGGTTCTGGCATGCTTTAGCAATgtgagtttac-attttgatttagactttgtttaagcttgtatatattgttgttagtcaatatttttaaataatgattctaaatattttcttcatttcttttctgtag

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 5
TGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaaccagtccctttctga-gaataatatacctccatttcgttatggtcgtt----tttctcataagatgtatgtcgccaatgaatttgcag
|||||| ||||| || |||||||||||  ||||||| || ||||||||  |||||||||| ||||||||||||||||||||| | ||||| || || || ||  || |   | |     | ||  |||   | ||  |   ||| |  |  ||  |     ||| |   ||  | | |||   |  |   | |||||
TGTGAGGCCTTTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGCATTGATGGTCCAAGTGAGGGTGTTCCTCGGGTTCTTGCATGCTTTAGCAATgtcagttacttacttttgctatgttgaagtttttagatgattttagccagagttttgaaaatttgttcaaaattttctgttttcctttg-tctgcag

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 5
TGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaaccagtccctttctgagaataatatacctccatttcgttatggtcgtttttctcataagatgtatgtcgccaatga--atttgcag
||| ||||| ||||| ||||||||||| || ||||| || || |||||  ||||||||||||| |||||||| || |||||| | || || || ||||||||| ||  ||  |     | |    ||| |  |   | | | || |    |  | ||  ||  |  | | ||  |      ||   |||| |||
TGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAACgtaagtatacaggcttagtcc----aatgacctgagttcttctcatggctgcagcttaacttttttg-tttaactttttggtgggtattttcag

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 5
TGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaaccagtccctttctgagaataatatacctccatttcgttatggtcgtttttctcataagatgtatgtcgc-caatgaatttgcag
|||||| || || || |||||||| || |||||||| |||||||||||  ||||||||||||| ||||| |||||  ||||| ||||||| |||||||| ||  ||       ||  |         || ||    |   |||| || |  |  |  |  || |    | | | || | ||||          
TGTGAGGCCCTTTAACTGGATTGGGCCCAGAATGGATTTTATTCCTGGCATTGATGGTCCTAGCGAGGGCGTTCCAAGGGTTCTGGCATGCTTCAGTAATgttagtttcaacatctgtcataacatttagtagtattttttttctttttcttactactgatcttgctctttttctcccacaatag--------

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 5
TGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaaccagtccctttctgagaataatatacct--ccatttcgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcag
|||||| ||||| || |||||||| || |||||||| || ||||||||  |||||||||||||||| ||||||||  ||||| ||||||| ||||| || ||  ||    ||    || ||  |  ||    |   |     | |  || |  |  ||||| ||        |          |      | ||
TGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGAAGGTGTTCCAAGGGTTCTGGCATGCTTCAGCAATgttagtt--tcaacatctgtcataacatggcttgtttggtagtatttttttcattttttttgtctctgatcttgctctttttctcccaccgtag

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|58677005|gb|CK065692.1|CK065692
EST:     TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTAGGCATGTTTCAGTAAC                         AATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
genomic: TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
EST: gi|58675034|gb|CK063721.1|CK063721
EST:     TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAAC                         AATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
genomic: TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
EST: gi|58587635|gb|CF985943.1|CF985943
EST:     TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAAC                         AATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGGCAGTCCCAG
genomic: TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
EST: gi|58587411|gb|CF985719.1|CF985719
EST:     TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAAC                         AATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
genomic: TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
EST: gi|25801443|gb|CA757404.1|CA757404
EST:     CTCGGGTTTTGGCATGTTTCAGTAAC                         AATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
genomic: CTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
EST: gi|58655446|gb|CK044126.1|CK044126
EST:     TTGATGGTCCTAGTGAGGGTG-TCCTCGGGTTTTGGCATGTTTCAGTAAC                         AATCTCCTGCGTCGGGAGCCCCTGAAGGTTGTTGATGGTGGCCAGTCCCAG
genomic: TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG

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), 51 (downstream exon)
Score: 16

TGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA




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