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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagcacttatgtaattatgttttggaataaatagaacgtaatcttgggaagcataattttgcatgagctgaaaaataaaattatgcagctgtttctagactgcaatgcctggtatgggaaactttttattttctccaaagtagctaaactacctatctctttctgcagCTTCTCTTATGTCGTGACGATCTTCAATGTCTGTCCACACGAAGTGTCTATTGAAATCCATGATCTCGCTTCGTTGGGGCTTGAATTGCATCCTATTCAG

Basic information

species Oryza sativa
transcript LOC_Os04g08270.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g08270.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G158043_T01 (Zea mays), 3'ss of exon 25
gtaagtagcacttatgtaattatgttttggaat-aaatagaacgtaatcttgggaagcataattttgcatgagctgaaaaataa----aattatgcagctgtttctagactgcaatgcctggtatgggaaactttttattttctccaaagtagctaaactacctatctctttctgcagCTTCTCTTATGTCGTGACGATCTTCAATGTCTGTCCACACGAAGTGTCTATTGAAATCCATGATCTCGCTTCGTTGGGGCTTGAATTGCATCCTATTCAG
||||| | || |  | || |||| ||   |  |    ||    ||| |||     |  ||| |||      |  ||| || ||     |||  |  || | | |  |        |  ||| || ||    ||||| ||  | || | |   ||||||           ||| ||||| ||||||| |||||| ||  |||||||||| |||||  ||||||||||||| ||||||| |||||| || ||  || ||||| | ||||||||  | |||
gtaagcaacattgttatatttatattccagccttgggtattgtgtattct-----attata-tttactggaaattgagaagtagttacaatattttagttatctgcacttctatgtatctgctacggaggtcttttgatgatgtctacaaaggctaaatgggtacgtgttttttgcagATTCTCTTGTGTCGTTACAGTCTTCAATGTATGTCCGTACGAAGTGTCTATAGAAATCCCTGATCTTGCATCACTGCGGCTTCAGTTGCATCCAGTGCAG
















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|86437343|gb|CI119065.1|CI119065
EST:     ATTAAAGATGCTCAAAATGAAAAATGTAAAATGGCTCAGTTAGATAAAAA                         CTTCTCTTATGTCGTGACGATCTTCAATGTCTGTCCACACGAAGTGTCTAT
genomic: ATTAAAGATGCTCAAAATGAAAAATGTAAAATGGCTCAGTTAGATAAAAAgtaagtagca ... ctttctgcagCTTCTCTTATGTCGTGACGATCTTCAATGTCTGTCCACACGAAGTGTCTAT




















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: 473

GCTTTCACAACACAGGTCCCTCGATGGTACCAGGAGTTATTGTCATGAGCATTAAAGATGCTCAAAATGAAAAATGTAAAATGGCTCAGTTAGATAAAAAgtaagtagca ... ctttctgcagCTTCTCTTATGTCGTGACGATCTTCAATGTCTGTCCACACGAAGTGTCTATTGAAATCCATGATCTCGCTTCGTTGGGGCTTGAATTGCATCCTATTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgggaaactttttattttctccaaagtagctaaactacctatctctttctgcagCTTCTCTTATGTCGTGACGATCTTCAATGTCTGTCCACACGAAGTGTCTATTGAAATCCATGATCTCGCTTCGTTGGGGCTTGAATTGCATCCTATTCAG
                            agctaaa  putative branch site (score: 473)
                                   ctacctatctctttct  CT-rich tract
     aaactttttattttct  TA-rich tract