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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacattttctgttgatgatacattgaaatttaccatatattcaatgggatctgaaaatccttcattgggaaggatgcttgcattgctttacactattcagtaggctgacgtctttggtttgaattttgacagAGAGCATGCACCATCCATAATCTTTATGGATGAAATAGACTCCATTGGATCTGCTAGAATGCAGTCAGGATCTGGGGGTGGTGATAGTGAGGTTCAACGC

Basic information

species Oryza sativa
transcript LOC_Os06g39870.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
gtaaacattttctgttgatgatacattgaaatttaccatatattcaatgggatctgaaaatccttcattgggaaggatgcttgcattgctttacactattcagtaggctgacgtctttggtttgaattttgacagAGAGCATGCACCATCCATAATCTTTATGGATGAAATAGACTCCATTGGATCTGCTAGAATGCAGTCAGGATCTGGGGGTGGTGATAGTGAGGTTCAACGC
| | | || |||| | | ||| | || | ||||| | ||| | | || | | | || | || | || | |||| |||||||||||||| ||||||||||||||||| || ||| |||||||||||| | ||| | |||||| ||| |||||||||||| || || ||
------------------------------gtagagcccatcatcaacaataacaaaaagga---aaaaaaaaatgttgctttctttgttgctgtttgttta--aactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG

upper sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------gtaaacattttctgttgatgatacattgaaatttaccatatattcaatggg-----atctgaaaatccttcattgggaaggatgcttgcatt--gctttacactattcagtaggctgacgtctttggtttgaattttg----------acagAGAGCATGCACCATCCATAATCTTTATGGATGAAATAGACTCCATTGGATCTGCTAGAATGCAGTCAGGATCTGGGGGTGGTGATAGTGAGGTTCAACGC
| | ||||| | || | | | | | || || | |||| | | | | | || || | ||| ||| | |||| | | | || | |||| | | || |||| |||||||| ||||| || ||||| ||||||||||| ||| |||||||||||| ||||| | || ||| |||| |||||||||||| || || ||
gtttgtttaatatctttagtggaaaccatgacttgtgatacacctagaggatttatttttcactcataagataatattttatatgttacctctcctgggtaattgtttagagtcacatttttttcctgggttattgaattttgttttaaatctcccttttatcttgtccttatggtctcttctctgctgctttattacagGGAGCATGCTCCATCAATCATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGAATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGA
















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|58612276|gb|CK039988.1|CK039988
EST:     TATATTGGAGAGGGTTCCAGAATGGTTCGTGAACTATTTGTGATGGCCAG                         AGAGCATGCACCATCCATAAT
genomic: TATATTGGAGAGGGTTCCAGAATGGTTCGTGAACTATTTGTGATGGCCAGgtaaacattt ... attttgacagAGAGCATGCACCATCCATAAT
EST: gi|29655700|gb|CB651975.1|CB651975
EST:     TATATTGGAGAGGGTTCCAGAATGGTTCGTGAACTATTTGTGATGGCCAG                         AGAGCATGCACCATCCATAATCTTTATGGATGCAATAGACTCCATTGGATC
genomic: TATATTGGAGAGGGTTCCAGAATGGTTCGTGAACTATTTGTGATGGCCAGgtaaacattt ... attttgacagAGAGCATGCACCATCCATAATCTTTATGGATGAAATAGACTCCATTGGATC
EST: gi|29655701|gb|CB651976.1|CB651976
EST:     TATATGGGAGAGGGTTCCAGAATGGTTCGTGAACTATTTGTGATGGCCAG                         AGAGCATGCACCATCCATAATCTTTATGGATGAAATAGACTCCATTGGATC
genomic: TATATTGGAGAGGGTTCCAGAATGGTTCGTGAACTATTTGTGATGGCCAGgtaaacattt ... attttgacagAGAGCATGCACCATCCATAATCTTTATGGATGAAATAGACTCCATTGGATC

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), 75 (downstream exon)
Score: 10

ACACCGACTGTACCTTTATTAGGGTGTCAGGTTCCGAGTTGGTTCAGAAGTATATTGGAGAGGGTTCCAGAATGGTTCGTGAACTATTTGTGATGGCCAGgtaaacattt ... attttgacagAGAGCATGCACCATCCATAATCTTTATGGATGAAATAGACTCCATTGGATCTGCTAGAATGCAGTCAGGATCTGGGGGTGGTGATAGTGAGGTTCAACGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcattgctttacactattcagtaggctgacgtctttggtttgaattttgacagAGAGCATGCACCATCCATAATCTTTATGGATGAAATAGACTCCATTGGATCTGCTAGAATGCAGTCAGGATCTGGGGGTGGTGATAGTGAGGTTCAACGC
                         ggctgac  putative branch site (score: 10)
 tttgaatttt  TA-rich tract