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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaatatttaccagaaatctgttgcatctattttatttagatagatttatattacaggaatttttgaatagctgccagatttcttccttcctaatgacatgcacctctatttgggcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTCATCGCTTCTTTGCTGAGCTCCCAATCGCCCGAACGG

Basic information

species Oryza sativa
transcript LOC_Os09g33600.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 13
gtacaaatatttaccagaaatctgttgcatctattttatttagatagatttatattacaggaattt-ttgaatag------ctgccagatttcttccttcctaatgacatgcacctctatttgggcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTCATCGCTTCTTTGCTGAGCTCCCAATCGCCCGAACGG
|||  ||  || |    | || | |   |||| |||  |||| | ||  | || ||| | |||  | || |||||       ||  | |||  || ||  ||| |||  ||||     | ||| ||||||||||||||| ||||||||||||||||||||||||||||| || || ||||| |||||||||||||||||||| || || ||||| 
gtatgaagcttaaatgcatatgt-tgatatctgtttc-tttatacaggatgatgttatatgaagctgttcaatagacatacttgtgatattgatttctgtctagtgatgtgcattggaaattgtgcagGCAGAGAGTGCAATGGATCAGATGGATTGGATTGAAAAAATTACCGGCGTCATTGCTTCTTTGCTGAGCTCCCAGTCTCCTGAACGA

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 13
gtacaaatatttaccagaaatctgttgcatctattttatttagata-gatttatattacaggaatttttgaatagctgccagatttcttccttcctaatgacatgcacctctatttgggcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTCATCGCTTCTTTGCTGAGCTCCCAATCGCCCGAACGG
                |  || |  ||  | | ||  ||||   |   ||| |||  |      |  || ||  |||      |||| |  | | ||||   ||||     | |  | |||||||||||||||| |||| || |||||||||||||||||||| |||||||| || ||||| || ||||| || ||    || ||  ||
----------------gttatttaatgtgttttttggatttttttttaattcatacaaggatggtgattaaa--gctttatagtttcat--tccttaat--tatgc----ttgtcagtgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAGATTCCTGATAGG

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 13
gtacaaatatttaccagaaatctgttgcatctattttatttagatagatttatattacaggaatttttgaatagctgccagatttcttccttcctaatgacatgcacctctatttgggcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTCATCGCTTCTTTGCTGAGCTCCCAATCGCCCGAACGG
                               || |  ||| | | | || ||  | ||| | | ||| | ||   |  ||    || ||  ||        | |   |   | |   ||||||||| | |||  |||| |||||||||||||| ||||| ||||||||||| || ||  | ||  ||||  | ||| | |        
------------------------------gtactc-attcaaaaaaatcta-gtgacacgtactttggcatt-ttatcattactcctctgtctcctcactaagg--ccaaaataatgcagGCAGAAAATGCCCTGGACCAGATGGATTGGATGGAAAAGATAACTGGTGTAATTGCCACCTTATTGAGTGCACAAACACTG------

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA06G17300.1 (Glycine max), 3'ss of exon 15
gtacaaatatttaccagaaatctgttgcatctattttatttagatagatttatattacaggaatttttgaatagctgccagatttcttccttcctaatgacatgcacctctatttgggcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTCATCGCTTCTTTGCTGAGCTCCCAATCGCCCGAACGG
                                   | ||| | | | |||||  | ||| | | ||     |       |  | |||  ||  ||  | || |    |   | |   ||||||||| | |||  ||||||||||||||||||| ||||| ||||||||||| || || || ||  ||||  | ||| | |        
----------------------------------gtcattcaaaaaaattta-gtgacatgtacttgcattttatcattacttctctctctgtctcctcac-taaggccaaaataatgcagGCAGAAAATGCCCTGGATCAGATGGATTGGATGGAAAAGATAACTGGTGTAATTGCCTCCTTATTGAGTGCACAAACACTG------

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 13
gtacaaatatttaccagaaatctgttgcatctattttatttagatagatttatattacaggaatttttgaatagctgccagatttcttccttcctaatgacatgcacctctatttgggcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTCATCGCTTCTTTGCTGAGCTCCCAATCGCCCGAACGG
                |  || |  ||  |   ||  ||||   || ||| |||  |  |    |  | ||    |   || ||  ||||||  | |||           | |  | |||||||||||||||  |||| || ||||| |||||||||||||| |||||||| || ||||| || ||||| || |||   || ||| ||
----------------gttatttaatgtgttctttagattttttta-attcatac-atggatggtgattaaagctttatagtttcattccttaattatg---------cttgtcagtgcagGCAGAGAGTGCACTGGACCAAATGGACTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAAATTCCTGAAAGG

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 13
gtacaaatatttaccagaaatctgttgcatctattttatttagatagatttatattacaggaatttttgaa--tagctgccagatttcttccttcct-aatgacatgcacctct--------atttgggcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTCATCGCTTCTTTGCTGAGCTCCCAATCGCCCGAACGG---------
    |  | |  |   ||||     | ||| |  || |      |  |||| | ||  |||| |  |   |  | | ||     || | || | ||  ||||||  | |  | |        |||   | ||||||||| |||   |||||||||||| ||||| |||||||||||||| || || ||||||||| |||| | |||| | || ||| |          
--gtatgtttccaagtgaaaagatcttcattttcttcaacatattgaatttttcttttaggattcatgatactttggtgttctcttccatcatccccgaatgaccagaattttttaaatcttattgatgtagGCAGAGAATGCACAGGATCAGATGGACTGGATCGAAAAAATAACTGGAGTAATTGCTTCTTTGTTGAGTTTCCAAACACCTGAAAGAGCAATCATG

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 13
-----------------------------------------------gtacaaatattt---accagaaatc---tgttgcatctattttatttagatagatttatattacaggaatttttgaatagctgcca--gatttcttccttcctaatgaca--------tgcacctctatttgg----gcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTCATCGCTTCTTTGCTGAGCTCCCAATCGCCCGAACGG
                                                |  || |||||   ||| ||||     | ||   |  ||  |  |  || | | | ||   |  |  | || | ||  | |   |  ||||| || ||  ||| ||           || || | |  |||      ||||||||||||||  |||| || ||||||||||||||||| ||||| || || || ||||| || ||||| || ||  | || ||  ||
gtaaatcttacagcttaggttgcactcatgaagttcagtttacttctttgaaattatttgatacctgaaactgtatttttgcttgatggttctgtgaaatactgatggaatggtgaattgttaagtgttattattgatttttttctcactagtgctcattaatgttgtacatttgcttgtcagcacagGCAGAGAGTGCACTGGACCAAATGGATTGGATTGAAAAGATAACAGGGGTTATTGCTTCATTACTGAGTTCTCAGGCTCCTGAGAGG

upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 13
------------------------------------------------------gtacaa-atatttaccagaaa-tctgttgcatctattt---tatttagatag-atttatattacaggaatttttgaatagctgc--cagatttcttccttcctaatgacatgcacctctatttgggcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTCATCGCTTCTTTGCTGAGCTCCCAATCGCCCGAACGG
                                                       || |  ||| |||   |||  || |    |||        || ||    || | | ||  |   ||| | | | | || ||    |||||| ||  |  | | ||   |  ||| |  ||    ||||||||||| |||  ||||||| ||||| ||| ||||||| |||||||| || || ||||||||| |||| ||| |  | |  ||| ||
gtacaaaatcaaaggttagatcaaaaatataaatttgggttttcattcatgtttttagactatacttatatgaagctcagcattatcagcccaaatacttgtccagtactaatgctg-gggattatgtcagtacctagagcagatt-ctctcaactttatatta-acacttgaat----gcagGCAGAGAATGCACTGGATCAAATGGACTGGGTTGAAAAGATAACTGGAGTAATAGCTTCTTTGTTGAGTTCCGACGCACTTGAAAGG

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|58667459|gb|CK056145.1|CK056145
EST:     TGCGGTTCTGCTTCAGAATAATTTCTCCCACAAAAAACTACACTTTGCAG                         GCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTC
genomic: TGCGGTTCTGCTTCAGAATAATTTCTCCCACAAAAAACTACACTTTGCAGgtacaaatat ... atttgggcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTC
EST: gi|58669112|gb|CK057798.1|CK057798
EST:     TGCGGTTCTGCTTCAGAATAATTTCTCCCACAAAAAACTACACTTTGCAG                         GCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTC
genomic: TGCGGTTCTGCTTCAGAATAATTTCTCCCACAAAAAACTACACTTTGCAGgtacaaatat ... atttgggcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTC

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: 60 (upstream exon), 45 (downstream exon)
Score: 11

CGTGAACTTGCTAACATCAACCATTAAAGCTGATGCTGACCAATCGGATCTGCGGTTCTGCTTCAGAATAATTTCTCCCACAAAAAACTACACTTTGCAGgtacaaatat ... atttgggcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTCATCGCTTCTTTGCTGAGCTCCCAATCGCCCGAACGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaatagctgccagatttcttccttcctaatgacatgcacctctatttgggcagGCAGAGAGTGCGATGGATCAGATGGATTGGATTGAAAAAATAACTGGTGTCATCGCTTCTTTGCTGAGCTCCCAATCGCCCGAACGG
                         tcctaat  putative branch site (score: 11)
                                        cctctattt  putative PPT
               atttctt  TA-rich tract