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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtcgagtgataattaagcatatacttagatcaatagtcaattggttaataaactgctctgctgcag

Basic information

species Oryza sativa
transcript LOC_Os08g02330.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G036634_T01 (Zea mays), 5'ss of exon 13
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtcgagtgataattaagc----atatactta------------gatcaatagtcaattggttaataaactgctctgctgcag
|||||||||||||  |||||||| || || || || || ||||  ||||| ||||||||||||||||||||||||||    || |     ||  |       || | ||||             ||| |  ||  ||||| |||| |||  |  || | |||
GTTGTGGACTGTCACATGTGTGGAGACCCAAACTCAGTCCTTCAGTTTGCCTTCATAGAGTTCACTGATGAGGgtaatatatccatatccaaccagatttcaatttgcttactttgtgtaatgaatctactgttcattgggtaatgaacatccatgttccag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G166091_T01 (Zea mays), 5'ss of exon 6
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaa-gtg-----gtcgagtgataattaagcata--tact--------tagatcaatagtcaattggttaataaactgctctgctgcag
|||||||||||||| ||||||||||| || ||||| || ||| | |||||||||||||||||| |||||||||||||  |       || |   ||  || ||  |   ||||        | |||| |  ||  || || | | ||||  |  ||   |||
GTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCGCTGATGAGGgtaatatatccatatccaaccatgtttcagtttgcttactctgtgtaatggatctactgtttatcgggtgaaaaacatcgatgtcccag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G069102_T01 (Zea mays), 5'ss of exon 4
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtcga------gtgataattaagcata--tact--------tagatcaatagtcaattggttaataaactgctctgctgcag
|||||||||||||| ||||||||||| || ||||| || ||| | ||||||||||||||||||||||||||||||||    || |         ||  || ||  |   ||||        | |||| |  ||  || || | | ||||  |  ||   |||
GTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGGgtaatatatccatatcccaccatgtttcagtttgcttactctatgtaatggatctactgtttatcgggtgaaaaacatcgatgtcccag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G173428_T02 (Zea mays), 5'ss of exon 3
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtcgagtgataattaagc----atatactta------------gatcaatagtcaattggttaataaactgctctgctgcag
|||||||||||||| |||||||| || || || || || ||||| || || ||||||||||||||||||||||||||    || |     ||  |       || | ||||             ||| |  ||  ||||| |||| |||  |  || | |||
GTTGTGGACTGTCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGCCTTCATAGAGTTCACTGATGAGGgtaatatatccatatccaaccagatttcaatttgcttactttgtgtaatgaatctactgttcattgggtaatgaacatccttgttccag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G161649_T01 (Zea mays), 5'ss of exon 2
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtcgagtgataattaagc----atatactta------------gatcaatagtcaattggttaataaactgctctgctgcag
|||||||||||||| |||||||| || || || |  || ||||| ||  | ||||||||||||||||||||||||||    || |     ||  |       || | ||||             ||| |  ||  ||||| |||| | |  |  || | |||
GTTGTGGACTGTCGCATGTGTGGAGACCCAAACTTAGTCCTTCGGTTCACCTTCATAGAGTTCACTGATGAGGgtaatatatccatatccaaccagatttcaatttgcttactttgtgtaatgaatctactgttcattgggtaatgaccatccatgttccag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G456149_T01 (Zea mays), 5'ss of exon 6
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaa-gtg-----gtcgagtgataattaagcata--tact--------tagatcaatagtcaattggttaataaactgctctgctgcag
|||||||||||||| ||| ||||||| || ||||| || ||| | ||||||||| ||||||||||||||||||||||  |       || |   ||  || |   ||  ||||        | |||| |  ||  || || | | ||||  |  ||   |||
GTTGTGGACTGTCGCATGCGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCGTAGAGTTCACTGATGAGGgtaatatatccatatccaacaatgtttcaatttacttactctgtgtaatggatctactgtttatcgggtgaaaaacatcgatgtcccag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G398795_T01 (Zea mays), 5'ss of exon 6
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtcgagtgataattaagcatatacttagatcaatagtcaattggttaataaactgctctgctgcag
|||||||||||||  ||||||||||| || ||||  || ||| | ||||||||||||||||||||||||||||||||    |  |   |||   || ||| |  | ||                                      
GTTGTGGACTGTCACATGTGTGGGGACCCAAATTTAGTCCTTAGgtttgctttcatagagttcactgatgagggtaa----tatatccatatccaaccatgt-ttcag--------------------------------------

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G349794_T01 (Zea mays), 5'ss of exon 5
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaa-gtg-----gtcgagtgataattaagcata--tact--------tagatcaatagtcaattggttaataaactgctctgctgcag
|||||||||||||| ||||||||||| || ||||| || ||| | |||||||||||||||||||||||||| |||||  |       || |   ||  || ||  |   ||||        | |||| | |||  || |  | | ||||  |  ||    ||
GTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGATGgtaatatatccatatccaaccatgtttcagtttgcttactatgtgtaatggatctacagtttatcgagtgaaaaacatcgatgtccaag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G069102_T03 (Zea mays), 5'ss of exon 4
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtcga------gtgataattaagcata--tact--------tagatcaatagtcaattggttaataaactgctctgctgcag-----------
|||||||||||||| ||||||||||| || ||||| || ||| | ||||||||||||||||||||||||||||||||    || |         ||  || ||  |   ||||        | |||| |  ||  || || | | ||||  |  ||   |||           
GTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGGgtaatatatccatatcccaccatgtttcagtttgcttactctatgtaatggatctactgtttatcgggtgaaaaacatcgatgtcccagagggtgcaaga

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G457231_T01 (Zea mays), 5'ss of exon 6
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaa-gtg-----gtcgagtgataattaagcata--tact--------tagatcaatagtcaattggttaataaactgctctgctgcag
|||||||||||||| ||||||||||| || ||||| || ||| | |||||||||||||||||| |||||||||||||  |       || |   ||  || ||  |   ||||        | |||| |  ||  || || | | ||||  |  ||   |||
GTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCGCTGATGAGGgtaatatatccatatccaaccatgtttcagtttgcttactctgtgtaatggatctactgtttatcgggtga-aaacatcgatgtcccag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G014573_T01 (Zea mays), 5'ss of exon 2
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaa-gtg-----gtcgagtgataattaagcata--tact--------tagatcaatagtcaattggttaataaactgctctgctgcag
|||||||||||||| ||||||||||| || ||||| || ||| | |||||||||||||||||||||||||| |||||  |       || |   ||  || ||  |   ||||        | |||| | |||  || || | | ||||  |  ||   |||
GTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGATGgtaatatatccatatccaaccatgtttcagtttgcttactatgtgtaatggatctacagtttatcgggtgaaaaacatcgatgtcccag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G376619_T01 (Zea mays), 5'ss of exon 5
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaa-gtg-----gtcgagtgataattaagcata--tact--------tagatcaatagtcaattggttaataaactgctctgctgcag-----------------------------------------------------------------------------------------
|||||||| ||||| ||||||||||| || ||||| || ||| | ||||||||||||||||||||||||||||||||  |       || |   ||  || ||  |   ||||        | |||| |  ||  || || | | ||||  |  ||   |||                                                                                         
GTTGTGGAGTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGGgtaatatatccatatccaaccatgtttcagtttgcttactctgtgtaatggatctactgtttatcgggtgaaaaacatcgatgtcccagagggtgcaagggctgctctgaatctgtcaggaaccgtgcttggatattatcctatcaatgttctaccgtcaaaaactgcattgcaccag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G044246_T02 (Zea mays), 5'ss of exon 4
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaa-gtg-----gtcgagtgataattaagcata--tact--------tagatcaatagtcaattggttaataaactgctctgctgcag
|||||||||||||| ||||||||||| || ||||| || ||| | ||||||||||||||||||||||||||||||||  |       || |   ||  || ||  |   ||||        | |||| |  ||  || || | | ||||  |  ||   |||
GTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGGgtaatatatccatatccaaccatgtttcagtttgcttactctgtgtaatggatctactgtttatggggtgaaaaacatcgatgtcccag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G132286_T01 (Zea mays), 5'ss of exon 3
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtcgagtgataattaagc----atatactta------------gatcaatagtcaattggttaataaactgctctgctgcag
|||||||||||||  |||||||| || || || || || ||||| ||  | ||||||||||||||||||||||||||    || |     ||  |       || | ||||             ||| |  ||  ||||| |||| |||  |  || | |||
GTTGTGGACTGTCACATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCACCTTCATAGAGTTCACTGATGAGGgtaatatatccatatccaaccagatttcaatttgcttactttgtgtaatgaatctactgttcattgggtaatgaacatccatgttccag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G175541_T02 (Zea mays), 5'ss of exon 4
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtcgagtgataattaagc----atatactta------------gatcaatagtcaattggttaataaactgctctgctgcag
|||||||||||||| ||||||||||| || ||||| || ||| | ||||||||||||||||||||||||||||||||    || |   | ||  | |      | | ||||            |||| |  ||  || || | | ||||  |  ||    ||
GTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGGgtaatatatccatatacaaccatgtttcagtttgcttactctgtgtaatggatctactgtttatggggtgaaaaacatcgatgtcctag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT4G10610.2 (Arabidopsis thaliana), 5'ss of exon 4
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgta-----agtggtcgagtgataattaagcatatacttagatcaatagtcaattggttaataaactgctctgctgcag-------
||||| ||||||||||| ||||| ||||| || || || ||| | ||||||||||| |||||||||||||| ||||     |||       ||  |  |    ||    | |   |  ||     |||||| ||    ||   |  ||          
GTTGTTGACTGTCGTATATGTGGTGATCCCAACTCAGTACTTAGGTTTGCTTTCATCGAGTTCACTGATGAAGgtatcattagtttctctatgtaatctgtttattggataatgcctgtaagtgcttggtttatggtttgtcattttgggacttgtag

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G32790.2 (Arabidopsis thaliana), 5'ss of exon 4
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgta-------agtggtcgagtgataattaagcatatacttagatcaatagtcaattggttaataaactgctctgctgcag
||||| |||||||| || || || || || || || || ||||| ||||| |||||||||||||||||||| ||||       | |      ||  |     | |||     ||   || | || || ||  |  |    |  | | | |   
GTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAGgtattatttcattttctcggttctggagtatcatcagtgtactacagtggttaaatgtcttgtggttttgttttcag---

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 5
GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtcgagtgata-attaagcatatac------ttagatcaatagtcaatt--ggtt--aataaactgctctgctgcag----------------
||||| ||||||||||| ||||| ||||| ||||| ||||| || ||||| ||| | || || ||||||||||||| ||  |    | ||  ||| |   | |||      ||  | ||||  || |||  ||||  |    | |    | |   |                 
GTTGTTGACTGTCGTATATGTGGTGATCCTAATTCCGTTCTCCGATTTGCCTTCGTTGAATTTACTGATGAGGgtatgttctgaccttatgtatttaatctttaccgtctatttaagcaatgatcgattttggtttgaccccattaaatttccaaaaaagtgattttcattcc

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|86899176|gb|CI298078.1|CI298078
EST:     TTCGTTTTGCTTTCATAGAGTTCACTGATGAGG                         AGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
genomic: TTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtc ... tctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
EST: gi|29646834|gb|CB651841.1|CB651841
EST:     GGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG                         AGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
genomic: GGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtc ... tctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
EST: gi|29643786|gb|CB648793.1|CB648793
EST:     GGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG                         AGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
genomic: GGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtc ... tctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
EST: gi|29646833|gb|CB651840.1|CB651840
EST:     GGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG                         AGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
genomic: GGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtc ... tctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
EST: gi|218493611|gb|FG968673.1|FG968673
EST:     GATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTNGATGAGG                         AGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTAT
genomic: GATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACT-GATGAGGgtaagtggtc ... tctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTAT

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: 48 (upstream exon), 71 (downstream exon)
Score: 82

GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtc ... tctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC




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