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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaaagtggtctgatcatttgaaatatgtgatcgcctcttgatgttagtagttctaagaaattctttccgtaatgaaagttttattaaataaatcaagaaaataaaatcctaattctctttaacatttccaaatattttgcagGCTATTCTTTTATTTCAGAAAATAGAAGGTGTGGAAGTATGCTTATTTGGCATGTATGTCCAAGAATATGGTGCAGAATGCAAATTCCCAAACCAACGTC

Basic information

species Oryza sativa
transcript LOC_Os06g49130.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 11
gtgagaaagtggtctgatcatttgaaatatgtgatcgcctcttgatgttagtagttctaagaaattctttccgt-aatgaaagttttattaaataaatcaagaaaataaaatcctaattctctttaacatttccaaatattttgcagGCTATTCTTTTATTTCAGAAAATAGAAGGTGTGGAAGTATGCTTATTTGGCATGTATGTCCAAGAATATGGTGCAGAATGCAAATTCCCAAACCAACGTC
                                                     ||  | ||||| |   |   | |||   |   | ||  ||| | | ||  |   | | |  |   |  | ||| | |||| |      || ||||   || | || ||||| || ||||||||||||||||| ||| |||||||||||||||| ||||||| |||  | |||||  |||| || || || || |
-----------------------------------------------------gtgatgagaaagttgatttatcaatctgatcgtaatcgaatca-ttaatcatgaatattatttgatgcccttagc-tttcta------ttccagGTAGTTTTGTTGTTTCAAAAGATAGAAGGTGTGGAAGTTTGCCTATTTGGCATGTATGTTCAAGAATTTGGATCTGAATGTCAATTTCCTAATCAGCGCC

upper sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 9
gtgagaaagtggtctgatcatttgaaatatgtgatcgcctcttgatgttagtagttctaagaaattctttccgtaatgaaagttttattaaataaatcaagaaaataaaatcctaattctctttaacatttccaaatattttgcagGCTATTCTTTTATTTCAGAAAATAGAAGGTGTGGAAGTATGCTTATTTGGCATGTATGTCCAAGAATATGGTGCAGAATGCAAATTCCCAAACCAACGTC
                                                  |||     |||   ||  ||  |   |     | ||  |||  || ||   |  ||  | ||   ||| |  | |   |||     |   || ||||  ||  | || |||||||| || |||||||||||||||||| | |||||||||||||| ||||| | |||  | |||||  |||| || || ||||| |
--------------------------------------------------gtaaagggaagg--ttgctttagagctagtcatgttggtaatcaagtcgttattatttattctggattttgatgac--ttttggtttccatttcagGTAATCTTGTTGTTTCAGAAGATTGAAGGTGTGGAAGTATGCCTCTTTGGCATGTATGTTCAAGAGTTTGGATCTGAATGTCAATTTCCGAATCAACGGC

upper sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 9
gtgagaaagtggtctgatcatttgaaatatgtgatcgcctcttgatgttagtagttctaagaaattc--tttccgtaatgaaagttttattaaataaatcaagaaaataaaatcctaattctctttaacatttccaaatattttgcagGCTATTCTTTTATTTCAGAAAATAGAAGGTGTGGAAGTATGCTTATTTGGCATGTATGTCCAAGAATATGGTGCAGAATGCAAATTCCCAAACCAACGTC
                                                     ||  |  |||| |   |||     ||   | | | || |||| | | ||  |   | | |  | |||| |||  |  |||| |      || ||||   || | || ||||| |  ||||||||||||||||| ||| |||||||||||||||| ||||||| |||  | |||||  |||| || || || || |
-----------------------------------------------------gtgatgggaaagttgattttatccatccgattgtaatcaaatca-ttaatcatgaatacttttgattccctt--agctttcta------ttccagGTAGTTTTGTTGTTTCAAAGGATAGAAGGTGTGGAAGTTTGCCTATTTGGCATGTATGTTCAAGAATTTGGATCTGAATGTCAATTTCCTAATCAGCGCC

upper sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgagaaagtggtctgatcatttgaaatatgtgatcgcctcttgatgttagtagttctaagaaattctttccgtaatgaaagttttattaaataaatcaagaaaataaaatcctaattctctttaacatttccaaatattttgcagGCTATTCTTTTATTTCAGAAAATAGAAGGTGTGGAAGTATGCTTATTTGGCATGTATGTCCAAGAATATGGTGCAGAATGCAAATTCCCAAACCAACGTC
                   |       | | || | |  ||||  |  |  |  ||||      ||  ||   |||| |     || |    || || | |    |  | |   || |  | |   |||||       |||| ||||| ||||| || |||||||| || |||||||| ||||||||||||||||||||||||||||| |||| |||  |||| |     |  || || || || |
-----------------gtacagattgtgtatgcttggttcttatttcttttccttctt-----tttgttttctaattatgaccttct--gctacatgatgcctgttgactatcaacttccatactcattt-------tttttcagGCCATTCTGTTGTTTCAGAAGATTGAAGGTGTTGAAGTATGCTTATTTGGCATGTATGTCCAGGAATTTGGAACAGATTCTGCGTCTCCCAATCAGCGCC

upper sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgagaaagtggtctgatcatttgaaatatgtgatcgcctcttgatgttagtagttctaagaaattctttccgtaatgaaagttttattaaataaatcaagaaaataaaatcctaattctctttaacatttccaaatattttgc-agGCTATTCTTTTATTTCAGAAAATAGAAGGTGTGGAAGTATGCTTATTTGGCATGTATGTCCAAGAATATGGTGCAGAATGCAAATTCCCAAACCAACGTC
                      | | |    | |  || | ||| ||||| |   | ||    ||  | | ||| ||     |||| |  | |   ||  |    || |||  |  |||||  |  |||  |    |||||| | |||   |||| || ||||| || || ||||| || ||||||||||||||||| ||||| ||||||||||  ||| | ||||||  ||| || || ||||| |
---------------------gtaagaatgatcaaggcgtattgttgttactgtatttactgcata-tatgcgttat-----ttttctggagttcctctcg----tacaattatccttctcactcccatgccattttatttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGGATGTACGTCCAAGAATTCGGTTCTGAATGCGCATTTCCCAATCAACGCC

upper sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgagaaagtggtctgatcatttgaaatatgtgatcgcctcttgatgttagtagttctaagaaattctttccgtaatgaaagttttattaaataaatcaagaaaataaaatcctaattctctttaacatttccaaatattttgcagGCTATTCTTTTATTTCAGAAAATAGAAGGTGTGGAAGTATGCTTATTTGGCATGTATGTCCAAGAATATGGTGCAGAATGCAAATTCCCAAACCAACGTC
                       | || |  |||||| | |      | | |   | |      |  | |||  | | ||  ||||    | |          | ||| ||| |  |  |  |  ||||||     |||||  ||||   ||||  | || ||||| ||||||||||| ||||||||||| ||||| |||||||||||||||| |||  | |||||   |   || || ||||| |
-----------------------gtaaga-atgatcgacgcacaccatcattgtatttgct---tcatgtccacatttaatattttcaggattcctctcttgtagtaatatcgt--tcgtgctccacattt-----tatttatcagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGGATGTATGTCCAAGAATTTGGATCCGAATGTTCAAATCCCAATCAACGCC

upper sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 8
gtgagaaagtggtctgatcatttgaaatatgtgatcgcctcttgatgttagtagttctaagaaattctttccgtaatgaaagttttattaaataaatcaagaaaa-taaaatcctaattctctttaacatttccaaatattttgcagGCTATTCTTTTATTTCAGAAAATAGAAGGTGTGGAAGTATGCTTATTTGGCATGTATGTCCAAGAATATGGTGCAGAATGCAAATTCCCAAACCAACGTC
                                                     ||    || |  | | |    | |  | ||||| | | |||  | |  || | | ||||  | |    ||  |   | ||    |  ||| ||||  ||| | || |||||||| || ||||| || ||||||||||||||||| |||||||| ||||||| |||  |||||||   ||||||||| |||||||
-----------------------------------------------------gtatgcagga--tgtatattaagttgatgttttttcatatagttgacaaagacttaaattatga---actgaagattgtctttttcgtttccagGTAATTTTGTTGTTTCAGAAGATTGAAGGAGTAGAAGTATGCTTATTTGGGATGTATGTTCAAGAATTTGGATCAGAATGTCTATTCCCAAATCAACGTC

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: 53 (upstream exon), 45 (downstream exon)
Score: 3

AGTTGTTTCATCAGTGGACAAGAAACTGGAAGTTAAACCACATTTTTTCAAGATTTTGCAAGAGGACAATTATCCAGCTGAGTTCCCTTACAAGTCTAAGgtgagaaagt ... tattttgcagGCTATTCTTTTATTTCAGAAAATAGAAGGTGTGGAAGTATGCTTATTTGGCATGTATGTCCAAGAATATGGTGCAGAATGCAAATTCCCAAACCAACGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaatcaagaaaataaaatcctaattctctttaacatttccaaatattttgcagGCTATTCTTTTATTTCAGAAAATAGAAGGTGTGGAAGTATGCTTATTTGGCATGTATGTCCAAGAATATGGTGCAGAATGCAAATTCCCAAACCAACGTC
                              tttaacatttccaaat  TA-rich tract