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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACGGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatatttatttttaatttttttgtcaaaatgccaggtaaggaatgatctaggttatatatgaatcacaacttctgaagtgctctaatggtttcttgttattatcag

Basic information

species Oryza sativa
transcript LOC_Os09g32220.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G014313_T02 (Zea mays), 5'ss of exon 5
CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACGGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatatttatttttaatttttttgtcaaaatgccaggtaaggaatgatctaggttatatatgaatcacaacttctgaagtgctctaatggtttcttgttattatcag
| || || |||||||||||||||| | |||||||||||||||||||||| ||||| |||||||| ||||||||||| ||||||||||| ||||| |||||||  |||||   | | || |  ||| ||||||             |||| | || | |  ||||   |  |  |  ||| ||   |||||||| | |  |||||     ||
CAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATGGGATTGACCTGAGCACTGTTGATGTCAGCTATGTTAGTAGCCGGTCATGgtatgtata--aaatatttacctttatgtcaa------------tgaattaccttgatggtatagcgactaggatctctaaa--tctctaatg-tctgctgttaccgatag

upper sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ16068 (Selaginella moellendorffii), 5'ss of exon 5
CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACGGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgta--tatttatttttaatttttttgtcaaaatgccaggtaaggaatgatctaggttatatatgaatcacaacttctgaagtgctctaatggtttcttgttattatcag
| || ||||| || ||  | || |   ||||| | || ||| ||||||| || || ||| ||||  | || |||||||||||||| ||||||||||||||||  |    ||   |  || | |||  |  ||    ||    |  ||                                                                  
CCAAAATTCCTTTCCCGCTCACGCAAAGATTCCGAGGGATGTTGCAAAATGGAATCGACTTGAGCTCGGTGGATGTGAGCTATGTCAGCAGCCGTTCATGgtaagctgctagcaaggttaagtttcatgctcggtgtgtatcgacag------------------------------------------------------------------
















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|88834677|gb|CI077960.1|CI077960
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|86511384|gb|CI154017.1|CI154017
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|89195920|gb|CI007339.1|CI007339
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|86525680|gb|CI165886.1|CI165886
EST:     GTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|66920739|gb|CX107587.1|CX107587
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|86834746|gb|CI340863.1|CI340863
EST:     TGTTAGCAGCCGTTCAT-                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: TGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|88206181|gb|CI206030.1|CI206030
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|88214287|gb|CI214136.1|CI214136
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|87032311|gb|CI264092.1|CI264092
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|87017018|gb|CI286154.1|CI286154
EST:     TAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: TAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|25806351|gb|CA762312.1|CA762312
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTTTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|86523056|gb|CI163262.1|CI163262
EST:     TGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: TGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|4716728|gb|AU057844.1|AU057844
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|86528191|gb|CI168397.1|CI168397
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|86506491|gb|CI149124.1|CI149124
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|86854905|gb|CI260973.1|CI260973
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|86545313|gb|CI185519.1|CI185519
EST:     GCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|86836282|gb|CI348237.1|CI348237
EST:     TAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: TAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|88829310|gb|CI074180.1|CI074180
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|86543296|gb|CI183502.1|CI183502
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|88270574|gb|CI385832.1|CI385832
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCACCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGT
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|117242276|gb|CT842928.1|CT842928
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|86417257|gb|CI031466.1|CI031466
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|86523141|gb|CI163347.1|CI163347
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|88252682|gb|CI351110.1|CI351110
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCACCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|33665107|gb|CF296074.1|CF296074
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|33688253|gb|CF316492.1|CF316492
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
EST: gi|86251662|gb|CI016951.1|CI016951
EST:     GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATG                         GTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG
genomic: GGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGG

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), 64 (downstream exon)
Score: 46

CTAAGATTCCCTTTCCATTGACTCCGCGATTCAGGGGAATGCTGCAAAACGGGATAGACCTGAGTACTGTTGATGTGAGCTATGTTAGCAGCCGTTCATGgtgcgtatat ... ttattatcagGTACTTTCTCAATTTGTTTGGTTTGAGGGGTCTCTTCAGTCTGATCCTCGGTGAAGAAAATG




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