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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggaccatgcttcatttgagcctgtttactattgtcttgtgtgattcttatgcatttccgatcttttgtcatccag

Basic information

species Oryza sativa
transcript LOC_Os01g55360.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55360.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 11
ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggaccat----gcttcattt-----gag------cctgtttacta------ttgtcttgtgtgattcttatgcatttccgatcttttgtcatccag
|||||||||||||| |||||||||||||| ||||| ||||||||  | || || |||| |||||||||| |||||||||| ||||| |||| | |     |||  |||     |||      ||  ||   ||      || |||| ||| ||| | |  || |  | | ||||| |||| |||
ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcgttatcactttttttatcttgagtggttcccccttctttaagcagtttatcttttgtcattgtaac-caatgtctaccttttctcattcag

upper sequence: LOC_Os01g55360.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G452529_T03 (Zea mays), 5'ss of exon 3
ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggaccatgcttcatttgagcctgtttactattgtcttgtgtgattcttatgcatttccgatcttttgtcatccag-------------------------
|||||||||||||| |||||||||||||| ||||||||||||||  | || || |||| |||||||||| |||||||||| ||||| |||| |||   | | || |   | |||| |  | |   |  |  || ||||||| ||   ||||| |||||| |                           
ATGGTTATGGCAGTGTTTGCATACATATACCACCAATCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcat-tattacttaattttatttatt--tattgcggttcttttttatgcaattt--atcttctgtcattctaacaaatgtgtacctttttcattcag

upper sequence: LOC_Os01g55360.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA10G32660.1 (Glycine max), 5'ss of exon 10
ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggaccatgcttcatttgagcctgtttactattgtct-tgtgtgattcttat---gcatttccgatcttttgtc-atccag-------------------
||||||||||| || ||||||||||||||||| || |||||  |   ||| ||||    ||| |||||  | || ||||| |||||    |  ||  || |||| |   ||| || || | | | | |||  |||| |     |||||  ||| |||  |  ||  |                    
ATGGTTATGGCCGTGTTTGCATACATATATCATCAGTCATTTGTTGTGCCGCAAACTCTCTCGGTTGAAATGATTTTGGACCAGgt---aattata-tttattttactatgtatattactttgtatatgtatttctaaattaacatttaagatgtttaatttatggaactgccgctgttcgcttcag

upper sequence: LOC_Os01g55360.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA20G34940.1 (Glycine max), 5'ss of exon 11
ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggaccatgcttcatttgagcctgtttactattgtcttgtgtgattcttatgcatttccgatcttttgtcatccag-----------------------
||||||||||| || |||||||| |||||||| ||||||||  |   ||| ||||    ||| |||||  | || ||||| ||||| |  |   |  ||    | ||  | ||   |  | | |||| |   | |||   |   || |   | | | ||  |                        
ATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCGCAAACTCTCTCAGTTGAAATGATTTTGGACCAGgtaattatgcttattttactaagtatattgctttgtat-ttgtatttctattaattaacacctaagatgtttaatttatggcactaccactgtttgcttcag

upper sequence: LOC_Os01g55360.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G62430.1 (Arabidopsis thaliana), 5'ss of exon 11
ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcag----------gaccatgcttca---tttgagcctgtttactattgtcttgtgtgattcttatgcatttccgatcttttgtcatccag
|||||||||||||| ||||| ||||||||||  |||||||| ||     |||||| |   || |||||   |||| | || ||||| |           |||  ||  |||    |  |   | || ||| |||   ||  | |||       |  |  |||  |||    |  ||
ATGGTTATGGCAGTATTTGCCTACATATATCTTCAATCATTTATTGTCTCCCAAAGCGTTTCGGTTGACAAAATCCTAGACCAGgtaaatgaacttctcgactttgtatcaaaactgaaaaatattcacttttgcactgaatcattgaatcaaacatgtgatggtttcat-tgtag

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|88990260|gb|CI107686.1|CI107686
EST:     AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|88828918|gb|CI073788.1|CI073788
EST:     AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|89162878|gb|CI099768.1|CI099768
EST:     AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|86437554|gb|CI119276.1|CI119276
EST:     AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|89198721|gb|CI003458.1|CI003458
EST:     AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|88844663|gb|CI021238.1|CI021238
EST:     AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|29679198|gb|CB675473.1|CB675473
EST:     AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|88258926|gb|CI359316.1|CI359316
EST:     GTTGAGCTAATCTTGGAACAG                         ATTGTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: GTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|86504386|gb|CI147019.1|CI147019
EST:     AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|88994295|gb|CI117249.1|CI117249
EST:     ATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: ATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|29681975|gb|CB678250.1|CB678250
EST:     AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|88254829|gb|CI351457.1|CI351457
EST:     ACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: ACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|29671304|gb|CB667579.1|CB667579
EST:     AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|313081133|gb|HO213719.1|HO213719
EST:     AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|86433541|gb|CI093884.1|CI093884
EST:     AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
EST: gi|88959995|gb|CI381873.1|CI381873
EST:     AATCATTCATATCGCCCCAAAACTACTCTTTTGAGCTAATCTTGGAACAG                         ATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT
genomic: AATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTT

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: 49 (upstream exon), 69 (downstream exon)
Score: 2

ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggacca ... tgtcatccagATTCTAAGAAATCTAACCTTTGAGGAGCAGAAATTCTTATATCAGCAGCTTGGGGAAATCTACCGTGAAAGGCAATTAATGCAGAGCTGAGAACTAGTTT




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