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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatctttacatcgaaaggatttacactggaaattaaatattgtagaagaaatggtgctgacaaacatttctgtacactaatgcagAATTGCCGGAGAGATCTTATGGAGCTGACTGCCGTCTGTATGTTCCGGAAAACCCTAAAAACAAGTTCATAAATATTTAT

Basic information

species Oryza sativa
transcript LOC_Os05g48060.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g48060.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G131994_T01 (Zea mays), 3'ss of exon 4
gtaatatctttacatcgaaaggatttacactggaaattaaatattg----------tagaagaaa-----tggtgctgacaaacatttctgtacactaatgcagAATTGCCGGAGAGATCTTATGGAGCTGACTGCCGTCTGTATGTTCCGGAAAACCCTAAAAACAAGTTCATAAATATTTAT
|||| || | | |  | ||  | || |||    |  | | |||||           || || |||     ||||| | | |||| |||       | |||||||||||||| ||||||| |||||||||||| || |||||||||||||| |||||||||||||||||||||||||||||||||
gtaaaatttctgcgccaaatagtttcacaagaaatgtaatatatttctttcttttttaaaaaaaagacggtggtgataataaaccttttgtctttccaatgcagAATTGCCAGAGAGATGTTATGGAGCTGATTGTCGTCTGTATGTTCCAGAAAACCCTAAAAACAAGTTCATAAATATTTAT

upper sequence: LOC_Os05g48060.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G477340_T03 (Zea mays), 3'ss of exon 6
gtaatatctttacatcgaaaggatttacactggaaattaaatattg---------tagaagaaa-----tggtgctgacaaacatttctgtacactaatgcagAATTGCCGGAGAGATCTTATGGAGCTGACTGCCGTCTGTATGTTCCGGAAAACCCTAAAAACAAGTTCATAAATATTTAT--------------------
|||| || | | |  | ||  | || |||    |  | | |||||          || || |||     ||||| | | ||||||||       | |||||||||||||| |||||||||||||||||||| |||||| |||||||||| |||||||||||||||||||||||||||||||||                    
gtaaaatttctgcgccaaatagtttcacaagaaatgtaatatatttctttttttttaaaaaaaagatggtggtgataataaacattttgtctttccaatgcagAATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAAACCCTAAAAACAAGTTCATAAATATTTATGTATGATTTTTCTGTATGAA

upper sequence: LOC_Os05g48060.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G477340_T01 (Zea mays), 3'ss of exon 6
gtaatatctttacatcgaaaggatttacactggaaattaaatattg---------tagaagaaa-----tggtgctgacaaacatttctgtacactaatgcagAATTGCCGGAGAGATCTTATGGAGCTGACTGCCGTCTGTATGTTCCGGAAAACCCTAAAAACAAGTTCATAAATATTTAT
|||| || | | |  | ||  | || |||    |  | | |||||          || || |||     ||||| | | ||||||||       | |||||||||||||| |||||||||||||||||||| |||||| |||||||||| |||||||||||||||||||||||||||||||||
gtaaaatttctgcgccaaatagtttcacaagaaatgtaatatatttctttttttttaaaaaaaagatggtggtgataataaacattttgtctttccaatgcagAATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAAACCCTAAAAACAAGTTCATAAATATTTAT

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: 50 (upstream exon), 48 (downstream exon)
Score: 10

AACCGCGATGATGCTCGCCAGTTCATGAAACACCTTTACCCTGATCTTGGAGTTGgtaatatctt ... actaatgcagAATTGCCGGAGAGATCTTATGGAGCTGACTGCCGTCTGTATGTTCCGGAAAACCCTAAAAACAAGTTCATAAATATTTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaaatattgtagaagaaatggtgctgacaaacatttctgtacactaatgcagAATTGCCGGAGAGATCTTATGGAGCTGACTGCCGTCTGTATGTTCCGGAAAACCCTAAAAACAAGTTCATAAATATTTAT
                                            cactaat  putative branch site (score: 10)
     aatattgta  TA-rich tract