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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG

Basic information

species Oryza sativa
transcript LOC_Os09g07510.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
gtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG
                                                      | |  ||  |  | | | | |||  |||||         || ||    |  |||||||      |||   | | | | || || ||  |  ||       | |||  |||   |||| || |||||||| |||||||| |||||||| |||||| | |||||||| || || || ||||||||||| |   | ||
------------------------------------------------------aaagatacatagaaaaaataatt--ttgct-------tttgctgtctagtattgcttccaa-aaatgaagttctaca-ttttgtcacatagta----gaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 4
gtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatattta-tttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG
                                                       |||||| |||||   |||| ||  ||   ||||   |  | |||| ||        | |    | | | |||   || |||||  ||   ||| | ||    |  |  |  |||||| || || ||||| || ||||| |||||||| ||||||||||||||||| || || || || || ||||||| | | ||
-------------------------------------------------------tatttagtttgcctgcatttatatgtctgtagaatgttat-atgcaccataccaaatat----tcttttttatt-tatttatgtgat---ttaatttc----atcc--tggatagGATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 3
gtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataa-ttatgacatcttttactctctgtaactcattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG
                                                      | | |||  |  | | ||| |||  |||||         ||  |    |  ||||||| |    |||  || | | |  || | ||||  || |       | |||  |||   |||| || |||||||| |||||||| |||||||| |||||| | |||||||| || || || ||||||||||| |   | ||
------------------------------------------------------aaagttacatagaaaaattaatt--ttgct-------tttgccgtcttgtattgcttc-gaaaaatgaatttctacatcttgtcacatagttga------attacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 4
gtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG
                                                         ||  | | |   |||||||  ||   || |   |  | |||| ||     |    | || | | | | |   || |||||  ||   ||| | ||    |  |  |  |||||| || || ||||| || ||||| |||||||| ||||||||||||||||| ||||| || || || ||||||| | | ||
---------------------------------------------------------ttagtctccctgcattcatatgtctgtaaaatgttat-atgcaccataccgaa--tattttttttttaaatttatttatgtgat---ttaatttc----atcc--tggatagGATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGCGAAGCTGTAGGCCCTGAACCTACCAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 5
gtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG
                                                                 || ||    | || |||    |   | || ||      ||||     |||   |  | |     | |||    |||  | ||       |   |   | || |||| || || ||||| ||||| ||||||||||| |||||||| |||||||| || || || ||||||||||| | | | ||
-----------------------------------------------------------------caaactcatacta-ttgagtcataattctcataaaaatagttagaagtgtcaca-atatggt--ttatttgatcattgtgtatgagaaattttttcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv03s0038g00200.t01 (Vitis vinifera), 3'ss of exon 1
gtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaat------agGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG--------------------
                                                                                                                                       |  ||  | || ||  |  ||| | || || |      |||| || || ||||| ||||| ||||||||||| |||||||| |||||||| || || || ||||||||||| | | | ||                    
--------------------------------------------------------------------------------------------------------------------------------------gtagcacatatt-cttcccataaattatgaatttctctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0008g07090.t01 (Vitis vinifera), 3'ss of exon 2
gtaaattacacccctacttggtacctcagtgtcatctacttgatatcac-atataatatttatttgcagacattcatta-gttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaat------agGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG
                                      | |   | ||| ||   ||| |   |||   || ||  | |   |  |  ||||      |     ||   || | |   |  |  | |||||| | |   |   | | | |   |  ||| | || || |      |||| || || ||||| ||||| ||||||||||| |||||||| |||||||| || || |                      
----------------------------------cgatcctagaaccactatgctatagtagcttggctactttagtaatagtatttaaggtataaattttgttgatacgcctttaaagc-taagctaccatgagTCGCATCACATATTCCTCCCATAAATTATGAATTTCTCTCAGGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAG----------------------

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|300215963|gb|HO088589.1|HO088589
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
EST: gi|58654414|gb|CK043094.1|CK043094
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
EST: gi|58652709|gb|CK041389.1|CK041389
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
EST: gi|33654809|gb|CF277423.1|CF277423
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCA-                         GAC-AAT-ATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
EST: gi|58593044|gb|CF991352.1|CF991352
EST:     AATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATAGTGGTTGCCAATCAATTGTATGAGCT
genomic: AATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATA-TGGTTGCCAATCAATTGTATGAGCT
EST: gi|33796143|gb|CF323937.1|CF323937
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
EST: gi|58672176|gb|CK060862.1|CK060862
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCG
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCG
EST: gi|300215769|gb|HO088395.1|HO088395
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
EST: gi|33676187|gb|CF304426.1|CF304426
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC

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: 72 (upstream exon), 69 (downstream exon)
Score: 71

ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG
                                     ctgtaac  putative branch site (score: 71)
                                        taactcattaaata  TA-rich tract