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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcccttcataactagtacagtttatcaacctgtatccttgctcaagtttttaacgatgtaatgttctccgatttctctacagAAAAGGTGTTTGAGAAAACTGTGCCTTTTGCAACTTCAGTGCTGGATGGGTACAATGTTTGCATATTTGCTTATGGACAGACGGGCACTGGTAAAACATT

Basic information

species Oryza sativa
transcript LOC_Os12g42160.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42160.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G400223_T03 (Zea mays), 3'ss of exon 6
----------gtaaatcccttcataactagtacagttt---atcaacctgtatcc------ttgctcaagtttt--taacgatgtaatgttctccgatt-tctctacagAAAAGGTGTTTGAGAAAACTGTGCCTTTTGCAACTTCAGTGCTGGATGGGTACAATGTTTGCATATTTGCTTATGGACAGACGGGCACTGGTAAAACATT
           |  |  | ||  | |||      ||||   || |   |||||        ||||||| |||||   ||| || |  | |  ||   || | | |||||||||||| ||||||||||||| ||| | ||||| ||| ||| |||| || |  ||||||||||| ||||||||||| || || || ||||||||||||||
gtaactcactatgcaatctttatttacttaccttgtttcacattattttgtattgacgtgattgctcatgttttaacaacaattttttttattcaacttatatatacagAAAAGGTTTTTGAGAAAACTGCGCCATATGCAATTTCTGTGTTGGACGGATTTAATGTTTGCATCTTTGCTTATGGGCAAACTGGTACTGGTAAAACATT

upper sequence: LOC_Os12g42160.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G18590.1 (Glycine max), 3'ss of exon 10
gtaaatcccttcataactagtacagtttatcaacctgtatccttgctcaagtttttaacgatgtaatgttctccgatttc--tctacagAAAAGGTGTTTGAGAAAACTGTGCCTTTTGCAACTTCAGTGCTGGATGGGTACAATGTTTGCATATTTGCTTATGGACAGACGGGCACTGGTAAAACATT
     |     ||  | |  |  ||  |      ||| ||     | ||| |  | |       |   || |    |||   | || ||   |  | |||||  | || |  || |||||||| ||||| || ||||| |||||||| ||||| ||||| ||||||||||| || || || ||||| ||
----gtattgccaggaattctttaggatgaggttctgaattga-acacaaatgctcagtttaacagatttatttatttttcttttatagCTGATATTTTTGAAGACACAGCACCATTTGCAACCTCAGTTCTAGATGGATACAATGTATGCATTTTTGCATATGGACAGACTGGGACAGGAAAAACTTT

upper sequence: LOC_Os12g42160.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv19s0027g00080.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------gtaaatcccttcataactagtacagtttatcaacctgtatccttgctcaagtttttaacgatgtaatgttctccgatt-tctctacagAAAAGGTGTTTGAGAAAACTGTGCCTTTTGCAACTTCAGTGCTGGATGGGTACAATGTTTGCATATTTGCTTATGGACAGACGGGCACTGGTAAAACATT
                           |       | | |||| | |  |  | ||   ||| |    || |||||  | |  |  ||    |  | |  | || | |  ||||   | || |||||  | ||||  || |||||| | ||||| || |||||||||||||| || |||||||||||||| ||||| || || || || || ||
gtaatcacataaagtaaattttgtttttgttatattccctaaccaatttatataatgttcctttgggttttctcaacctgtgtattatcacttcctttgtgcttgtttgaacagCTGATGTTTTTGAAGACACTGCACCATTTGCAGCCTCAGTTCTAGATGGGTACAATGTCTGTATATTTGCTTATGGGCAGACTGGAACAGGGAAGACTTT

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), 27 (downstream exon)
Score: 4

TTTGAATCTGCAAAAGACGGCGAACTAATTGTCAGAGGGCATGTATCTTCAAAAAAGGTTTTCAAATTTGATTCTGTTTTCAGCCCTGAAGAAGATCAAGgtaaatccct ... ttctctacagAAAAGGTGTTTGAGAAAACTGTGCCTTTTGCAACTTCAGTGCTGGATGGGTACAATGTTTGCATATTTGCTTATGGACAGACGGGCACTGGTAAAACATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgtatccttgctcaagtttttaacgatgtaatgttctccgatttctctacagAAAAGGTGTTTGAGAAAACTGTGCCTTTTGCAACTTCAGTGCTGGATGGGTACAATGTTTGCATATTTGCTTATGGACAGACGGGCACTGGTAAAACATT
                    ttttaac  putative branch site (score: 4)
                                    ttctccgatttctct  putative PPT
                aagtttttaa  TA-rich tract