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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_Os09g07510.1
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG
                                     ctgtaac  putative branch site (score: 3)
                                        taactcattaaata  TA-rich tract