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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctctcttctgtcaactgtcatatctgaagacatttcgtattactatctctttggctcgtttttttttctcccaggctgttttcaggtattaactatttatttatttgtgacagGATCTGGTTTTGATGAGACAAAACAACATTAATGCTGTTAGAAACAGCCATTATCCCCAACATCCAAGGTGGTATGAGCTGTGTGACATTTTTGGACTTT

Basic information

species Oryza sativa
transcript LOC_Os01g72340.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G032496_T01 (Zea mays), 3'ss of exon 1
-gtagctctcttctgtca-actgtc--atatctgaagacatttcgtattactatctctttggctcgtttt--tttttctcccaggctgttttcaggtattaactatttatttatttgtgacagGATCTGGTTTTGATGAGACAAAACAACATTAATGCTGTTAGAAACAGCCATTATCCCCAACATCCAAGGTGGTATGAGCTGTGTGACATTTTTGGACTTT
   |      | |||||| | ||    | || | |||   |||   || |  ||||||||||   | |||  |  |   ||||||     ||||| |  | || || ||| |||||||||||||| ||| |||||||||| |||||||| || |||||||||||||| |||||||| || || || ||||||||||||||| | |||||||||||||| ||||
gtcaagatcttcctgtcatattggagaacattttaag-tttttaacataataatctctttggtctgatttaatcatatgcccagg-----ttcagattcttacaatatatctatttgtgacagGACCTGATTTTGATGAGGCAAAACAATATCAATGCTGTTAGAAATAGCCATTACCCACAGCACCCAAGGTGGTATGAGTTATGTGACATTTTTGGTCTTT

upper sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA13G26700.1 (Glycine max), 3'ss of exon 8
gtagctctcttctgtcaactgtcatatctgaagacatttcgtattactatctctttggctcgtttttttttctcccaggctgttttcaggtattaactatttatttatttgtgacagGATCTGGTTTTGATGAGACAAAACAACATTAATGCTGTTAGAAACAGCCATTATCCCCAACATCCAAGGTGGTATGAGCTGTGTGACATTTTTGGACTTT
|||   ||  ||| |       | |   | || |  | |    |||  ||      |||    |  | |||       | | |||| ||  | |||  |||  | |  ||   ||||||| |||| || ||||  |||||||| ||||||||||| || |||||||||||||||||||||||| | ||||||||||| |||||  | |||||  | |
gtactgctaatctttttttccccttcaataaaaaattgttagtttatgat------ggccaaatgctattt-------gtttttttaagacactaataattgctgtgctt---acagGATTTGGTCTTAATGAAGCAAAACAATATTAATGCTGTGAGGAACAGCCATTATCCCCAACATCCACGTTGGTATGAGCTATGTGATTTGTTTGGCATGT

upper sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv13s0067g03000.t01 (Vitis vinifera), 3'ss of exon 8
--gtagctctcttctgtcaactgtcatatctgaagacatttcgtattactatctctttggctcgtttttttttctcccaggctgttttc-aggtattaactatttatttatttgtgacagGATCTGGTTTTGATGAGACAAAACAACATTAATGCTGTTAGAAACAGCCATTATCCCCAACATCCAAGGTGGTATGAGCTGTGTGACATTTTTGGACTTT
  | | |   ||  |||    |||  | | || | |        ||   | | | ||  | |  | ||  |||     |   | || || || | || | || |   |    |   ||||||| ||||| | ||||  |||||||| || |||||||| ||||||||||||||||||||||||||  | ||||| ||| |||||||  | |||||  | |
gtgcaacctcctcttgt----tgttctctttggatat------catctttgtgtgttaagttaatgttggtttgattgatcatattgtcgagatcttcattactctctggcat---acagGATTTGGTTCTAATGAAGCAAAACAATATCAATGCTGTGAGAAACAGCCATTATCCCCAACATCCTCGATGGTACGAGTTGTGTGATTTGTTTGGCATGT

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: 68 (upstream exon), 72 (downstream exon)
Score: 25

GATGCTTGTCAATGGATGTCCTGTTGTAATAAGAGGTGTCAACAGACATGAGCATCATCCACGTGTTGGAAAGACAAATTTAGAAGCTTGCATGATTAAGgtagctctct ... tttgtgacagGATCTGGTTTTGATGAGACAAAACAACATTAATGCTGTTAGAAACAGCCATTATCCCCAACATCCAAGGTGGTATGAGCTGTGTGACATTTTTGGACTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttttctcccaggctgttttcaggtattaactatttatttatttgtgacagGATCTGGTTTTGATGAGACAAAACAACATTAATGCTGTTAGAAACAGCCATTATCCCCAACATCCAAGGTGGTATGAGCTGTGTGACATTTTTGGACTTT
                            tattaac  putative branch site (score: 25)
                                         tttattt  putative PPT
                    ttttcaggtattaact  TA-rich tract