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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGTTGAACCAGCTGATGAAAGGCGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtgctttgatcgcaactgttggctgctgtaataatagttgatttatcacttgaacatcaaattcctcagctcttttagaaacacaaccgttacgataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttttcttctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g67134.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67134.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G163081_T04 (Zea mays), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGCGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtgctttgatcgcaactgttggctgctgtaataatagt-tgatttatcacttgaacatcaaattcctcagctcttttagaaacacaaccgttacgataacctttggat-tgttgatctgtattagtagctcatgtggatatacttctcttttcttctgcag
|| |||||| ||||||||||| ||| ||||||||||||||||||||||||||||||| || ||||| || || || |||||||||||||||||||||||||| | |  |  | || | |  ||  |  | |  | || |  |    |  ||| |   | |  ||||||          | ||| |    |    | || |   | | || | | | || ||| |  | ||   | ||| | | |      |    |||  | | ||||
CTCTGTTGAGCCAGCTGATGAGAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTTATCAGGACTACAACAGGGAACCGTGTCTTTGGTGCCCTCAAGgtatat-atcttctgtttgttaccat--gatattatattggtgtcattgtttgtatttagcccatcaagaataatcattttttcatgtgc-ttgctgtaagagtcatctcttgttgtggtgaacgat-ttcccatctc-tctagcccctttaacgtttgttgccgcag

upper sequence: LOC_Os01g67134.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G815894_T03 (Zea mays), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGCGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtg--tgttgtgctttgatcgcaactgt-tggctgctgtaataatagttgatttatcacttgaacatcaaattcctcagctcttt-tagaaacacaaccgttacgataacctttg----gattgttgatctgtattagtagctcatgtggatatacttctcttttcttctgcag
|| |||||| ||||||||||| ||| ||||||||||||||||||||||||||||||| |||||||| || ||||| ||||||||||||||||||||||||||   |||  | ||||    |  |   | |      ||   |  | |||  |   |  ||     ||   | |  | |  | |||  |  |||         | |  | | |||     || || |  ||  | |  |||| |  |     | |  | |  | |  | ||||||
CTCTGTTGAGCCAGCTGATGAGAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTTATTAGGACTACAACTGGGAACCGTGTCTTTGGTGCCCTCAAGgtacatgtcttccttttgatgtcatgatgttatatttggggtgtttgtttgtagttagctcattaatagtaataataatttttttgcatgaacttgttgtacaaggcatcttttatggtgactggttttccatctctgtagttttttaacgtttgttgcattatgttgctgcag

upper sequence: LOC_Os01g67134.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGCGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtgctttgatcgcaactg-ttggctgc-tgtaataatagttgatttatcacttgaacatcaaattcctcagctcttttagaaacacaaccgttacgataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttttcttctgcag
|| ||| || ||||| || || ||| ||||||||||||| ||||| ||||| ||||| |||||||| || |||||||||||||||||||||||||||||||| | ||     || |||   | || |||  | | | | |||  | ||   || |   |||    |           |||  |  |||||         ||||||                                                               
CTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTCCGTGCCCTCTTAGATGTCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtatattccttctttatcatgaatgattgtatacatatgata-cattttccttgtgttttggttgtagg------tggcttatcaagaaaacttttttatacgatct-------------------------------------------------------------

upper sequence: LOC_Os01g67134.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G06590.1 (Glycine max), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGCGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtgctttgatcgcaactgttggctgctgtaataatagttgatttatcacttgaacatcaaattcctcagctcttttagaaacacaaccgttacgataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttttcttctgcag
 |  || ||||| |||||    ||| |||| |||||||||||| | |||||||| || |||||||| || || || |||||||| ||||||||||| |||||    | |  |   |  | || ||||      ||| ||  |  || | |  |   |  ||  | ||    ||  | |  |||| |                                                                                
TTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACCGGTAACCGTGTGTTTGGTGCCCTTAAGgtaatctatcat---actgtaa-tgttaatcagtgtgattttgttttaatggttgatcaaat-tgaataatctgtgattgtttacag-------------------------------------------------------------------------------

upper sequence: LOC_Os01g67134.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G06580.1 (Glycine max), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGCGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtg---tgttgtgctttgatcgcaactgttggctgctgtaataatagttgatttatcacttgaacatcaaattcctcagctcttttagaaacacaaccgttacgataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttttcttctgcag
 |  || ||||| |||||    ||| |||| |||||||||||| | |||||||| || |||||||| || || || |||||||| ||||||||||| |||||    | |  |||| | ||   ||    ||     | |  |||| ||||||  |    |||||     |||   | |    ||  ||                                                                                 
TTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACCGGTAACCGTGTGTTTGGTGCCCTTAAGgtaatctatcatgctgtaatgttaatcagtgtgattttttttaatggttgatcaaa---ttgaat----aatctgtgattgtttacag---------------------------------------------------------------------------------

upper sequence: LOC_Os01g67134.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA16G03170.1 (Glycine max), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGCGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtgctttgatcgcaactgttggctgctgtaataatagttgatttatcacttgaacatcaaattcctcagctcttttagaaacacaaccgttacgataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttttcttctgcag
 |  || ||||| |||||    ||| |||| |||||||||||| | |||||||| || |||||||| || ||||| |||||||||||||||||||| |||||    | |  |   |  |||| || |   || ||| ||  |  || | |  | |    |      ||||  | |    ||  ||                                                                                 
TTCAGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACTGGCAACCGTGTCTTTGGTGCCCTTAAGgtaatctatcat---actgcaa-tgctaattggtgtgattttgttttaatggtgatcaaattgaataattttttattgtttacag---------------------------------------------------------------------------------

upper sequence: LOC_Os01g67134.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT5G39740.2 (Arabidopsis thaliana), 5'ss of exon 6
CTATGTTGAACCAGCTGATGAAAGGCGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgt---gtgttgtgctttgatcgcaactgttggctgctgtaataatagttgatttatcacttgaacatcaaattcctcagctcttttagaaacacaaccgttacgataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttttcttctgcag
 | ||| |||||| |||||   ||  | ||||||||||||||  | |||||||| || || ||||| ||||||||||||||||| |||||||| ||||||||   ||||| |  | || | |    ||||     ||||  || ||||   || || | ||||| ||   || |      || |||| | || |    | |  | |   | |   | | | |                                               
TTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgttttaatgtggttgtctgtgttcttatctgttgta-tagtgtgttcatgatttgaagat--gatgctagcaatccttta-ataccctgttggtttgct--tcatgaaactatag-----------------------------------------------

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|58658098|gb|CK046778.1|CK046778
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|218502752|gb|FG953444.1|FG953444
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|218492462|gb|FG964263.1|FG964263
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|44667460|gb|CR280894.1|CR280894
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|33799084|gb|CF325402.1|CF325402
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATTGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGC
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGAT-GGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGC
EST: gi|29657555|gb|CB653830.1|CB653830
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|3768108|gb|AU032135.1|AU032135
EST:     TGGCCTCATTAGGACAACCACTGGAAACCCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TGGCCTCATTAGGACAACCACTGGAAA-CCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|33693282|gb|CF321521.1|CF321521
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGGTGGTCTTGACATTCCTCACAGTGAC
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGG-TGGTCTTGACATTCCTCACAGTGAC
EST: gi|58596831|gb|CK007359.1|CK007359
EST:     TTGGGCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGGCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|58686254|gb|CK074941.1|CK074941
EST:     GGGCCTCATTAGGACAACCACTGGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTGGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTGGCT
genomic: TGGCCTCATTAGGACAACCACTGG-AAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|29687293|gb|CB683568.1|CB683568
EST:     TTGGCCTCATTATGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|9884543|gb|BE607376.1|BE607376
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATG
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATG
EST: gi|33664337|gb|CF295304.1|CF295304
EST:     TTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|32948110|gb|BP184682.1|BP184682
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|117251436|gb|CT844165.1|CT844165
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|88974220|gb|CI019893.1|CI019893
EST:     CACTGGAAACCGTGTCTNTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: CACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|86851282|gb|CI312683.1|CI312683
EST:     CACTGGAAACTGTGTCTTTGGTGGCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: CACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|33823697|gb|CF337654.1|CF337654
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGGTGGTCTTGACATTCCTCACAGTGAC
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGG-TGGTCTTGACATTCCTCACAGTGAC
EST: gi|88385545|gb|CI564205.1|CI564205
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGG
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGG
EST: gi|58683059|gb|CK071746.1|CK071746
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|89186947|gb|CI053350.1|CI053350
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
EST: gi|29657556|gb|CB653831.1|CB653831
EST:     TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAG                         GGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT
genomic: TTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCT

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: 74 (upstream exon), 75 (downstream exon)
Score: 447

CTATGTTGAACCAGCTGATGAAAGGCGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtgtgttgtg ... tcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGT




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