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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggacttctaatctcctacaaacttaaagcatctcattaatttgcctttataagctaagaataatcttgtgttatcttctctttgcagAAATTATATGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g55974.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55974.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G124091_T04 (Zea mays), 3'ss of exon 6
gtttggacttctaatctcctacaaacttaaagcatctcattaatttgcctttataagctaagaataatcttgtgttatcttctctttgcagAAATTATATGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAG
||||||   | | |  ||||||| | ||| | ||  |||||||  |    | | ||| |   | |  | || |||  |  |   ||| |||||||| ||||| ||||||||||| |||||||| ||||| ||||||||||| |||
gtttggttgtttgag-tcctacacaattata-cacttcattaaacttttatcaaaagattt-actggttttatgtgtttattcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATTCAG

upper sequence: LOC_Os01g55974.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA05G03380.1 (Glycine max), 3'ss of exon 6
-----gtttggacttctaatctcctacaaactta--aagcatctcat--taatttgcctttataagctaagaataatcttgtgttatcttctctttgcagAAATTATATGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAG
        | || || ||| |    |  |  ||   || || || ||  |||  |       | | | |    |  | |  | || |||  ||  |||||    ||||||| |||||||| || |||||||| ||||||||||| || ||||||
aagattccttgagttataaacaaacagtatttttttaaccacctgatactaagatattccacttaacaactttttttttaatcttgtctgatcaatgcagCGGCTATATGTGACCATGTTTCCGTGCAATGAATGTGCTAAGATCATAATCCAG

upper sequence: LOC_Os01g55974.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G13950.1 (Glycine max), 3'ss of exon 6
---gtttggacttctaatc---tcctacaaacttaaagcatctcat--taatttgcctttataagctaagaataatctt-gtgttatcttctctttgcagAAATTATATGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAG
    |||  | || ||| |      ||  |  || || || || ||  |||          | | ||     |  | ||  | || ||   ||  |||||    ||||||| |||||||| ||||||||||| ||||||||||| || ||||||
ttccttttaagttataaacaaacagtattatttttaaccacctgatactaagagattccacttatctcttttttttttttatattgtccaatcaatgcagCGGCTATATGTGACCATGTTTCCCTGCAATGAATGTGCTAAGATCATAATCCAG

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: 39 (upstream exon), 40 (downstream exon)
Score: 3

CTATGTTGTTCATGCTGAGGTTAATGCTATTTTAAATACAAACCATGCTTCAGCGGCTGGACAGgtttggactt ... ctctttgcagAAATTATATGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattaatttgcctttataagctaagaataatcttgtgttatcttctctttgcagAAATTATATGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAG
 cattaat  putative branch site (score: 3)
                                    tgttatcttctcttt  putative PPT
                      taagaataat  TA-rich tract