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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGAAGATGATTTTGCTACTCTTGCTGACAAGTGTATTTTTCCTGGAGATGTTCTATGGGTTAAAGATTCCGAAATCTACGAGAACCGTGACATAGCAGgtgaagcaacaattgtaatgtgctgaacatttctgaaaaatgatattgttgatggttcatttttttctttgcccttgatgtttcag

Basic information

species Oryza sativa
transcript LOC_Os03g09270.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g09270.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G154621_T01 (Zea mays), 5'ss of exon 13
ATTGAAGATGATTTTGCTACTCTTGCTGACAAGTGTATTTTTCCTGGAGATGTTCTATGGGTTAAAGATTCCGAAATCTACGAGAACCGTGACATAGCAGgtgaagcaacaattgta--atgtgctgaac-atttctgaaaaatgatattgttgatggttcatttttttctttgcccttgatgt--ttcag
||||||||||||||||||||||||||||| ||| ||||||||||||| ||| |||| ||||| | ||| || ||||| || |||||||||||||| |||||||||  | ||| | ||   ||||   ||  |||||| ||||| || |||||||||||||     ||    |   | || ||||  |||||
ATTGAAGATGATTTTGCTACTCTTGCTGATAAGAGTATTTTTCCTGGGGATTTTCTCTGGGTCAGAGACTCTGAAATATATGAGAACCGTGACATTGCAGgtgaataatcaaatatatggtgtggcaaattatttctaaaaaaggagattgttgatggtttcaacttcaagtgatcgtttatgtgtttcag

upper sequence: LOC_Os03g09270.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G376074_T01 (Zea mays), 5'ss of exon 13
ATTGAAGATGATTTTGCTACTCTTGCTGACAAGTGTATTTTTCCTGGAGATGTTCTATGGGTTAAAGATTCCGAAATCTACGAGAACCGTGACATAGCAGgtgaagcaacaattgtaatgtgctgaaca-tttctgaaa----aatgatattgttgatggttcatttttttctttgcccttgatgtttcag
||||||| ||| || ||||||||||| |||||| |||| |||||||| |||||||| ||||| | ||| || |||||||  |||||||||||||||||||||| || | ||| | | ||||||  || | ||| |||||    |||||| |||||||||||||   || || || |   ||  ||||||||
ATTGAAGGTGACTTGGCTACTCTTGCCGACAAGAGTATCTTTCCTGGGGATGTTCTTTGGGTCAGAGACTCTGAAATCTTTGAGAACCGTGACATAGCAGgtgcagtagcaaatatgatgtgccaaataatttgtgaaagacaaatgatgttgttgatggttctaattgtttttcg---tttgtgtttcag

upper sequence: LOC_Os03g09270.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv04s0008g03170.t01 (Vitis vinifera), 5'ss of exon 12
ATTGAAGATGATTTTGCTACTCTTGCTGACAAGTGTATTTTTCCTGGAGATGTTCTATGGGTTAAAGATTCCGAAATCTACGAGAACCGTGACATAGCAGgtgaagcaacaat-tgtaatgtgctgaacatttctgaaaaatgatattgttgatggt--tcatttttttctttg----cccttgatgtttcag-------
||||| | |||   | | ||||||||||||| |  ||| |||||||||||| |||| ||||| |||||||| || ||| | ||| | || || || |||||| |   |    |   || |    |||||  ||  | | | |  | |  |||    |  | | |   | ||  |    |  | |    ||||        
ATTGATGGTGAAACTTCCACTCTTGCTGACATGAATATATTTCCTGGAGATCTTCTTTGGGTGAAAGATTCAGAGATCCATGAGTATCGGGATATTGCAGgtaagttattgctacatacttgaatgaactgttggggatatttgtttctttggaaatatttaatgagtcctaggagggctttggggaattcacatggttt

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: 67 (upstream exon), 65 (downstream exon)
Score: 31

ATTGAAGATGATTTTGCTACTCTTGCTGACAAGTGTATTTTTCCTGGAGATGTTCTATGGGTTAAAGATTCCGAAATCTACGAGAACCGTGACATAGCAGgtgaagcaac ... gatgtttcagATGAAATTTCGGAGCAGAAGGTTGTAGTACAGACTGAGGAAGGCTTTCGTGGGACTCTGTTGACATCTAGTGCTTCAGCTCAGCTTTGCCAGGATATATC




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