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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacctcagttatttatgagatataccatcatttcagatttttttttatctgattagttatttcatacaatggccagAAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG

Basic information

species Oryza sativa
transcript LOC_Os08g32630.5
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g32630.5 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM5G851815_T02 (Zea mays), 3'ss of exon 14
gtaacctcagttatttatgagatataccatcatttcag--attttttt----ttatctgattagttatttcatacaatggccagAAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG
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gtaacttaaggtacctaaaag-tacaccattgcatcaataattctattcatcttatatgaattttgatttccttcaatg-tcagAAACTAGGGGATTCGGTACTTCGGCCATTTCTACAG
















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|29670150|gb|CB666425.1|CB666425
EST:     CCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATTTTGAGTCGATGCAG                         AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG
genomic: CCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATTTTGAGTCGATGCAGgtaacctcag ... caatggccagAAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG
EST: gi|29670151|gb|CB666426.1|CB666426
EST:     CCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATTTTGAGTCGATGCAG                         AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG
genomic: CCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATTTTGAGTCGATGCAGgtaacctcag ... caatggccagAAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG
EST: gi|29677474|gb|CB673749.1|CB673749
EST:     CCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATTTTGAGTCGATGCAG                         AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG
genomic: CCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATTTTGAGTCGATGCAGgtaacctcag ... caatggccagAAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG
EST: gi|88847633|gb|CI018324.1|CI018324
EST:     AGTCGATGCAG                         AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG
genomic: AGTCGATGCAGgtaacctcag ... caatggccagAAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG
EST: gi|88841109|gb|CI001071.1|CI001071
EST:     CCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATTTTGAGTCGATGCAG                         AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG
genomic: CCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATTTTGAGTCGATGCAGgtaacctcag ... caatggccagAAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG
EST: gi|29679962|gb|CB676237.1|CB676237
EST:     CCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATTTTGAGTCGATGCAG                         AAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG
genomic: CCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATTTTGAGTCGATGCAGgtaacctcag ... caatggccagAAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG

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: 66 (upstream exon), 36 (downstream exon)
Score: 35

ATCATGGTTGTTCCAAAGAGCAATGTCAGCAAGGCCGCAGATCGATGTTTCCCCAACTTTTATCAATGAGCTTCTCTTTGCTAATTTTGAGTCGATGCAGgtaacctcag ... caatggccagAAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccatcatttcagatttttttttatctgattagttatttcatacaatggccagAAACTTGGGGATTCAGTACTTCGGCCATTTCTCCAG
                         atctgat  putative branch site (score: 35)
               atttttttttatctga  TA-rich tract