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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttggatgacagcaatggaaacctctcacttagtcagttgcaaattttttcatacctaggaacactatatatgtccatggggcttattattttactgtaccgttcatttttgttttgagtaaatttatgaattctgctaatcatatgctttgttagtgtttggctaatgtaatgaatggttttattctag

Basic information

species Oryza sativa
transcript LOC_Os06g20370.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G465169_T02 (Zea mays), 5'ss of exon 8
GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtat--gtttggatgacagcaatggaaacctctcacttagtcagttgcaaattttttcatacctaggaacactatatatgtccatggggcttattattttactgtaccgttcatttttgttttgagtaaatttatgaattctgctaatcatatg-ctttgttagtgtttggctaatgtaatgaatggttttattctag
||||||||||| |||||||| ||||||||||||||||||||||| || ||||| ||||| ||||| || ||||| ||||||||||||||||   |||   || | |||| || |  ||  | ||||  || |    || ||| | |||  | |     | | || ||    |  || ||| | || ||  | | |     ||  |  || ||    | |  ||  |||  ||| ||   ||| ||| ||| ||  | |                            
GATGACAACAGGTATAACTCTAGCCGAGGTGCCCACCTGAATCTGAAGCGTGCAGAAAAAGCTCGTATCCTTGTTAACAAGATTCCAGgtaccagttcaaattatagca-tgaatgccctttacttcatctgcaagaagtttgtgcattgcaaaatttattttacataa--aatggacttgt-atcttgatatgctagatatgct--ttatgttccattccattgatt--gctgatgtaatgtcttcgttcgtcctag----------------------------

upper sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G101874_T01 (Zea mays), 5'ss of exon 9
GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtat--gtttggatgacagcaatggaaacctctcacttagtcagttgcaaattttttcatacctaggaacactatatatgtccatggggcttattattttactgtaccgttcatttttgttttgagtaaatttatgaattctgctaatcatatgctttgttagtgtttggctaatgtaatgaatggttttattctag
||||||||||| |||||||| ||||||||||||||||||||||| || ||||| ||||| ||||| |||||||| |||||||||||||||||  |||   || | | || ||    ||  | ||||    || ||| ||    ||  | ||| | || |||                     ||||||| ||||   |  | || | | ||     ||| | | |  | ||||     |||| |   ||  |     ||| ||||||||  |  ||| || ||||
GATGACAACAGGTATAACTCTAGCCGAGGTGCCCACCTGAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAGgtatcagttcaaattataaca-tgatttccctttactt---tagctgcgaagaagtttgtgccttgcaaaact---------------------tatttta-tgtaaactgaacttgtatctt-----aatctgttaggtatgctt----tatgttccattgatt----gctgatgtaatgtcttctttcatcctag

upper sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA02G46450.3 (Glycine max), 5'ss of exon 8
GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgt-ttggatgacagcaatggaaacctctcacttagtcagttgcaaattttttcatacctaggaacactatatatgtccatggggcttattattttactgtaccgttcatttttgttttgagtaaatttatgaattctgctaatcatatgctttgttagtgtttggctaatgtaatgaatggttttattctag
||||| ||||| |||||  ||||| ||||||| ||| | || ||||||||||| || || ||||||||  | |||||||| ||||||||||| | ||  ||||     ||   || | |   |  |  | |||   | |  ||| ||  ||     |  | ||               |   |  ||| || |    |  | ||| | ||| || ||  |                                                                
GATGATAACAGGTATAATGCAAGCAGAGGTGCACACTTAAACCTCAAACGTGCAGAGAAAGCTCGGATATTGGTCAACAAAATTCCAGgtatttgttaaatga----gattataatcaccatcagatactgttcttattaatttaat--ctgctgtcgttgtaagcaaaacaaaatgatgccacattattggaataattttgtttctgttg-gtgaaaatgcag------------------------------------------------------------

upper sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA18G10090.1 (Glycine max), 5'ss of exon 10
GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgt-ttggatgacagcaatggaaacctctcacttagtcagttgcaaattttttcatacctaggaacactatatatgtccatggggcttattattttactgtaccgttcatttttgttttgagtaaatttatgaattctgctaatcatatgctttgttagtgtttggctaatgtaatgaatggttttattctag
          | |||||  ||||  ||||||| ||| | || ||||||||||| || || || |||||||| |||||||| ||||||||||| | ||| |||  || ||     |    | | ||  ||| ||   |   |    |  |||   |  | ||     |  ||   ||  |    | | | || |                                                                                           
----------GGTATAATGCAAGTAGAGGTGCACACTTAAACCTCAAACGTGCAGAGAAAGCCCGGATTCTGGTCAACAAAATTCCAGgtatttgttgaatgtgagaaactattattatttatttgatcaattattagcatcaa-actccttacatgatta-----gctcaaaaggggtgccgtatcattggaa------------------------------------------------------------------------------------------

upper sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT4G26760.1 (Arabidopsis thaliana), 5'ss of exon 8
GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttggatgacagcaatggaaacctctcacttagtcagttgcaaattttttcatacctaggaacactatatatgtccatggggcttattattttactgtaccgttcatttttgttttgagtaaatttatgaattctgctaatcatatgctttgttagtgtttggctaatgtaatgaatggttttattctag
||| | ||||| ||||   ||||||||||||| ||  ||||||||||  | ||||| || ||||||||||| |||| ||||||| | |||| |        | ||        |  | | |||    ||  |  || |    | | ||  | ||| |    |||  |   | | ||                                                                                                           
GATCAGAACAGGTATAGTGCAAGCCGAGGTGCGCATTTGAATCTCAAGAGAGCTGAGAAAGCTCGGATTCTGGTCAGCAAGATTACTGgtaagaacttccaaaagtctctcttagttattacta---cacatagaattaaactgagactgaagaatatatcatactttgtttgtgcaag--------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G55230.1 (Arabidopsis thaliana), 5'ss of exon 8
GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttggatgacagcaatggaaacctctcacttagtcagttgcaaattttttcatacctaggaacactatatatgtccatggggcttattattttactgtaccgttcatttttgttttgagtaaatttatgaattctgctaatcatatgctttgttagtgtttggctaatgtaatgaatggttttattctag
||| | ||||| || | | ||||| ||||||| ||| ||||||||||  | ||||| || ||||||||||| || | ||||||||| ||||||| | ||       ||   | |  | |||  || |    |||||| || | |  |  ||   |||   ||||     || ||   | || || |  | ||  |                                                                                        
GATCAGAACAGGTACAGCGCAAGCAGAGGTGCACACTTGAATCTCAAGAGAGCTGAGAAAGCTCGGATTCTGGTTAGCAAGATTCCTGgtatgtgtaga-----ataactaagatatatcatatact----tgcaaacttct-ctcatgtattcacatcttataaag--attggatcttttgttatg-tataaag----------------------------------------------------------------------------------------

upper sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S153_95V6.1 (Physcomitrella patens), 5'ss of exon 8
GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttggatgacagcaatggaaacctctcacttagtcagttgcaaattttttcatacctaggaacactatatatgtccatggggcttattattttactgtaccgttcatttttgttttga-gtaaatttatgaattctgctaatcatatgctttgttagtgtttggctaatgtaatgaatggttttattctag
||||| ||  ||| |    | |||  |||||| ||||| ||||||||||||||||| |||||||||       ||   ||  |||||||||||       | |  | ||  ||   |||  |||  || | || |              |  || || |     ||| |||| |  ||  ||   |  ||||  | | |||    | || |  |||||  ||| |                                                           
GATGAGAATCGATTTG---CTAGCAAAGGTGCTCACCTCAATCTCAAACGTGCTGAGAAGGCTCGGGCAGCGATCGCTAAACTTCCAGgtatga------ggcgcctatccaa---tctatctttatccgctgta-------------ttgtgatcattgcccttgttcatgtg--tttctaccatg-tgtaatgcttattgaactgttaacataaatgaatgcag----------------------------------------------------------

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|58653743|gb|CK042423.1|CK042423
EST:     TCAACAAGATTCCAG                         CACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG
genomic: TCAACAAGATTCCAGgtatgtttgg ... tttattctagCACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG
EST: gi|66924847|gb|CX111695.1|CX111695
EST:     GAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAG                         CACTTGTTGAAACTCTGGTGGCAAAGACCACGGCATGGGAGGAGAGCCGTG
genomic: GAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttgg ... tttattctagCACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG
EST: gi|3760183|gb|C97441.1|C97441
EST:     GAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTGAACAAGATTCCAG                         CACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGNGAGGAGAGCCGT
genomic: GAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttgg ... tttattctagCACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGG-GAGGAGAGCCGT
EST: gi|88583042|gb|CI699517.1|CI699517
EST:     GAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAG                         CACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG
genomic: GAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttgg ... tttattctagCACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG
EST: gi|58668066|gb|CK056752.1|CK056752
EST:     GAATCTCAAACGTGCTGAAAAAGCTCGGATTCTTGTCAACAAGATTCCAG                         CACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG
genomic: GAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttgg ... tttattctagCACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG
EST: gi|87031673|gb|CI259857.1|CI259857
EST:     GAATCTCANACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAG                         CACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG
genomic: GAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttgg ... tttattctagCACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG
EST: gi|218496732|gb|FG958311.1|FG958311
EST:     GAATCTCAAACGTGCTGAAAAAGCTCGGATTCTTGTCAACAAGATTCCAG                         CACTTGTTGAAACTCTGGTGGCAAAGACCAGGCCATGGGAGGAGAGCCGTG
genomic: GAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttgg ... tttattctagCACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG
EST: gi|58597733|gb|CK008261.1|CK008261
EST:     GAATCTCAAACGTGCTGAAAAAGCTCGGATTCTTGTCAACAAGATTCCAG                         CACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG
genomic: GAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttgg ... tttattctagCACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG
EST: gi|218488852|gb|FG965228.1|FG965228
EST:     GAATCTCAAACGTGCTGAAAAAGCTCGGATTCTTGTCAACAAGATTCCAG                         CACTTGTTGAAACTCTGGCTGGCAAAGACCA
genomic: GAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttgg ... tttattctagCACTTGTTGAAACTCTGG-TGGCAAAGACCA
EST: gi|88586562|gb|CI704268.1|CI704268
EST:     GAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAG                         CACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG
genomic: GAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttgg ... tttattctagCACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTG

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: 75 (upstream exon), 61 (downstream exon)
Score: 36

GATGACAACAGATATAACTCAAGCCGAGGTGCCCACCTGAATCTCAAACGTGCTGAAAAGGCTCGGATTCTTGTCAACAAGATTCCAGgtatgtttgg ... tttattctagCACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGA




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