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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag

Basic information

species Oryza sativa
transcript LOC_Os01g54080.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G124883_T01 (Zea mays), 5'ss of exon 5
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag
 ||||| |||||||||||| |||| ||||||||||||||||| || ||||| ||||||||||| ||||| |||||||| || ||||| || ||||||||||    ||| |  |     |    |  | | | ||||  ||   |    |  | | ||||| |||||   || ||   ||      | ||     ||||
ATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTACACAATGg----tacgagggcagggc----ttgaaataacaaagttgaaattgatataagccttggg-atattactaactgttgcttgacattgttttttcttag

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 5
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgac-tctcttatc-ttttaccctttag
 ||||| |||||||| ||| |||| ||||||||||||||||| || ||||| ||||||||||| ||||| ||||||||||||||||| || ||||||||||||   ||  | |       |  |||| | || |||  ||   || |||   || | || ||||||   |||||    ||   ||  ||||      |||
ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaag-acggcag-------agctcaaaatag-aaagttgaattgataatagtcgt-ggcgatattagtaattggtgcctgacattgttttttttcctag

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA05G35130.1 (Glycine max), 5'ss of exon 12
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag---
 | ||| || || ||| | || || ||||||||||| ||||| |  ||||| || || ||||| ||||| |||||||||||||| ||||| || ||||||||||  ||     | | | ||| |  |        | ||  |     |  | | ||||  |  ||| |    | | ||| | |  |   | |||||     
ATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGGTATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTATACAATGgtatgaac---cctctgaataaattgattttt---atctcatacatca--tgttattgaaggaattct----tcattctataagatgccaacctttctcag

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA08G01800.1 (Glycine max), 5'ss of exon 14
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttacta---ctgtttaactaattcaagacagcaaacctgctctg--ctaactatcattggggatattgtaaattgactctcttatcttttaccctttag
 |||   || |  ||||| |||||| |||| ||||||||||| | ||||||||| || ||||| ||||| |||||||| || ||||| ||||| || |||||||  | ||   | ||||||    ||  |    ||  | ||   ||    ||  || ||   |   |  |   |                            
ATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATATACGATGgtatgcattatatccgtttaatgctttttatgttgcgtatctagcctaatttacttagcaactgcttttctactag---------------------------

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA05G37800.1 (Glycine max), 5'ss of exon 14
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgta-aattgactctcttatcttttaccctttag
 |||   || |  ||||| |||||| |||| ||||||||||| | ||||||||| || ||||| ||||| ||||| || || ||||| ||||| || |||||||  | || | ||    ||||                ||| |  ||       ||| | || ||||  |||| |||     ||   ||  |   |||
ATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACCGGCTCGGGAAAGACATATACGATGgtatgcatta-tattcgtttaat----------------gctttttta-----tgttgcgtatcttgtctaatttacttagcaattgcttttctactag

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA13G33390.1 (Glycine max), 5'ss of exon 10
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag
 |   | || || ||| | || ||  ||||||| |||||||| || ||||| || || ||||| ||||| || ||||||||||| ||||| ||||||||||||   |    | | ||  ||  |||         | |   |  | |||     |||    ||  | |||   ||     |||| | |||        
GTATGCTGACATACAAGCCTTTATACGATCAGTACTTGATGGGTTTAATGTATGTATATTTGCTTATGGCCAGACTGGTTCAGGGAAAACTTACACAATGgtaagcaactttatatatatatatca------ttcatcattttagataaa-ggaattactcattctataa---gatgtcattatttcttag-------

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA07G10190.1 (Glycine max), 5'ss of exon 13
--TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgt-ttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag
   |     || || |||  ||| ||  ||||||| |||||||| || ||||| || || ||||| ||||| || ||||||| ||||||||| ||||||||||||   |    | | || ||  ||  |        ||  |  |  ||   ||                                               
GTGTATGTTGAAATACAAGATTTTATACGATCAGTGCTTGATGGCTTTAATGTATGTATATTTGCTTATGGCCAGACTGgtttaggaaaaacttacacaatggtaagcaactttatattcacacatatattgattttaatttaattcgccgtcttag--------------------------------------------

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA08G04580.1 (Glycine max), 5'ss of exon 6
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag
 | ||| || || ||| | || || ||||||||||| |||||||  ||||| || || ||||| ||||| |||||||||||||| ||||| || || |||||||  ||  |   | ||   |||   ||     | |     |  |   ||||    ||   | ||     |  |   |   | |||||  |      
ATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTATACGATGgtatgaac--cctctgaatatatt---gatttttatctcatacatcatgctattgaaggaattcttcattctataagatgccaacttttctcag----

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 5'ss of exon 13
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttact-act-gtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag
 || || |||||  ||||| | ||| ||||||||||||| || | |||||| || || ||||||||||| || || || ||||| ||||| |||||||||||| | | | ||| || || |    | |||    || ||      ||| | ||| ||||      ||| | | |||  | | |                 
ATTTTCAGATATAAAACCTCTTATTCGATCAGTTCTTGACGGGTACAATGTATGTATCTTTGCATATGGTCAGACAGGATCAGGGAAAACTTACACAATGgtactcattcactagtatatcacgattaagtggccagacaaatgatgcca-cta-cattcataccattatca-ttgtttttgtccag-------------

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: AT1G73860.1 (Arabidopsis thaliana), 5'ss of exon 13
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttact-actgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag
 || || || ||   |||  || |||| ||||| |||||||| | ||||||||| || ||||||||||| || || || ||||| ||||| || |||||||||| || | ||||||       ||   || || ||   | |   |   | || |  ||  |   || ||  ||   || ||| ||||| |        
CTTTTCAGACATAAGACCGCTGGTTAGGTCAGTACTTGATGGGTACAATGTTTGTATATTTGCATATGGCCAGACAGGATCAGGGAAAACTTATACAATGgtatgtattcactgtt------gtttctgagagtaagatttcatag--gaataacgctgatgcgcttttaccttcgttccctt-tctttcag-------

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 5'ss of exon 13
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag
 || || || |  ||||| ||| |  |||| ||||||||||| |  ||||| || || ||||| ||||| ||||||||||| || || ||||||||||||||||  |||  | | |   | | || | |  ||| |  || |  | ||  | ||| |    |  ||||  | ||  |    | || | ||        
GTTTTCTGACACTCAACCCTTGGTACGATCTGTTCTTGATGGCTATAATGTATGTATATTTGCTTATGGTCAAACTGGTTCGGGCAAGACATACACAATGgtatgaacttgtatatgttttagtctacatggcatatgtgtt--gatattt-tcaataaaaac-ttgtgtaatgtattgtctttcctctag-------

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ12333 (Selaginella moellendorffii), 5'ss of exon 9
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag
 |||   ||||  || || |||||  | |||||||||||||| | ||| || || |||||||| ||||| ||||| || || |||||||| ||||| ||||||||||  ||          ||   | ||| |||     |  |  |  | |  ||| |   ||  |                               
ATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTACACCATGgtatttatgac----------atattatacaacaa-----cattatttgcaactatttgctgtacag-------------------------------

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ19920 (Selaginella moellendorffii), 5'ss of exon 9
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag
 |||   ||||  || || |||||  | |||||||||||||| | ||| || || |||||||| ||||| ||||| || || |||||||| ||||| ||||||||||  ||        |||||  | ||| |||     |  |  |  | |  ||| |   ||  |                               
ATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTACACCATGgtatttatgaca-------taatt--atacaacaa-----cattatttgcaactatttgctgtacag-------------------------------

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ28715 (Selaginella moellendorffii), 5'ss of exon 10
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag
|||    |||   || ||||||||| |||| || |||||||| ||||| || || |||||||| |||||||| |||||||| ||||||||||| || ||||||       ||||  | ||   | | ||         ||   |     ||||   ||  |                                     
TTTTCTGGATGCGCAGCCTTTGATTCGATCGGTGCTTGATGGTTTCAACGTCTGTATTTTTGCGTATGGACAGACTGGTTCTGGAAAAACATATACTATGgtaa-----gctgtg-agctccgttaggat-----ttgtgtattaacgtctattgatgcag-------------------------------------

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ30678 (Selaginella moellendorffii), 5'ss of exon 10
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgactctcttatcttttaccctttag
|||    |||   || ||||||||| |||| || |||||||| ||||| || || |||||||| |||||||| |||||||| ||||||||||| || ||||||      |    | | ||   | ||||         ||   |     ||||   ||  |                                     
TTTTCTGGATGCGCAGCCTTTGATTCGATCGGTGCTTGATGGTTTCAACGTCTGTATTTTTGCGTATGGACAGACTGGTTCTGGAAAAACATATACTATGgta------aggtgtgagctccgttaagat-----ttgtgtattaacgtctattgatgcag-------------------------------------

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|58683961|gb|CK072648.1|CK072648
EST:     TTTGCATTTTGGCATATGGACAAACTGGTTCAGGAAAAACATACACAATG                         AGTGGACCAGGGACATCAAGAGAAGACTGGGGTGTTAACTATCGTGCTTTA
genomic: TTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttacta ... taccctttagAGTGGACCAGGGACATCAAGAGAAGACTGGGGTGTTAACTATCGTGCTTTA
EST: gi|66917351|gb|CX104199.1|CX104199
EST:     TTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATG                         AGTGGACCAGGGACATCAAGAGAAGACTGGGGTGTTAACTATCGTGCTTTA
genomic: TTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttacta ... taccctttagAGTGGACCAGGGACATCAAGAGAAGACTGGGGTGTTAACTATCGTGCTTTA
EST: gi|58684417|gb|CK073104.1|CK073104
EST:     TTTGCATTTTTGCATATGGACAAACTGGTTCAGGAACAACATACACAATG                         AGTGGACCAGTGACATCAAGAGAAGACTGGGGTGTTAACTATCGTGCTTTA
genomic: TTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttacta ... taccctttagAGTGGACCAGGGACATCAAGAGAAGACTGGGGTGTTAACTATCGTGCTTTA
EST: gi|58677888|gb|CK066575.1|CK066575
EST:     TTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATG                         AGTGGACCAGGGACATCAAGAGAAGACTGGGGTGTTAACTATCGTGCTTTA
genomic: TTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttacta ... taccctttagAGTGGACCAGGGACATCAAGAGAAGACTGGGGTGTTAACTATCGTGCTTTA
EST: gi|33675793|gb|CF304032.1|CF304032
EST:     TTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATG                         AGTGGACCAGGGACATCAAGAGAAGACTGGGGGTGTTAACTATCGTGCTTT
genomic: TTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttacta ... taccctttagAGTGGACCAGGGACATCAAGAGAAGACTGGGG-TGTTAACTATCGTGCTTT

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: 63 (upstream exon), 71 (downstream exon)
Score: 23

TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttacta ... taccctttagAGTGGACCAGGGACATCAAGAGAAGACTGGGGTGTTAACTATCGTGCTTTAAATGATCTGTTTGATATTTCTCTAAGTAGGAAAAATGCATTCTCATATG




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