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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatgttagctaaatttacttcatatatacttccatttaacaagaattcagatatagcaattgaaatatataattatgttctgtagcatgccagcaaataaacacattttgataattcttgattccaataaaatgtaaagaataaaataattatggaaacttattttttatttgttgcagAGAAGCATACTATTAGATTGCGAAGATCGGATCAAGAGTCTCCTTGCAGTTGTGTTTGAAAATTACAAGTCCTTGGATGAGAATTCTCCTACTGGTTTGT

Basic information

species Oryza sativa
transcript LOC_Os02g10490.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G107737_T01 (Zea mays), 3'ss of exon 11
gtaatatgttagctaaatttacttcatatatacttccatttaaca-agaattcagatatagcaattgaaatatataattatgttctgtagcatgcc-agcaaat----------aaacacattttgataattcttgattccaataaaatgtaaag----aataaaataattatggaaacttatttt-ttatttgttgcagAGAAGCATACTATTAGATTGCGAAGATCGGATCAAGAGTCTCCTTGCAGTTGTGTTTGAAAATTACAAGTCCTTGGATGAGAATTCTCCTACTGGTTTGT
      | | | |||| ||  ||  ||||||  || ||     |  |||| || || |||  ||||| || | || |  ||| || | |  ||    | |||||          ||| ||| |  |  || |   ||  |   || |||   | |    | ||  | |  |  |  | | | |||| || |||||| ||| |||| ||  |  |||| || ||||||||||| |||||||||||||||| | |||||||||||||||| ||  |||||||  ||||||| ||||| ||||
-----gtatcatctaagttctctctatatattattgcaaaactcggagaactcggagataa-aattgcaaaacattaaaatgctcggcaaaatatttaccaaatcatgtccacaaaatacactg-ggcaaattgagaaccttctacaattccaggtttcagtagtacacatcagttatcgtgttttgttctttgttacagCGAAGTATTTTGATAGACTGTGAAGATCGGATTAAGAGTCTCCTTGCAGCTCTGTTTGAAAATTACAAATCACTGGATGAATATTCTCCAACTGGCTTGT

upper sequence: LOC_Os02g10490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S6_22V6.1 (Physcomitrella patens), 3'ss of exon 13
gtaatatgttagctaaatttacttcatatatacttccatttaaca-agaattcagatatagcaattgaaatatataattatgttctgtagcatgccagcaaataaacacattttgataattcttgattccaataaaatgtaaagaataaaataattatggaaacttattttttatttgttgcagAGAAGCATACTATTAGATTGCGAAGATCGGATCAAGAGTCTCCTTGCAGTTGTGTTTGAAAATTACAAGTCCTTGGATGAGAATTCTCCTACTGGTTTGT
                  |       |||   |    ||||| || ||   |    |   |   || |  |   |  || | || | |      |  |||  |     ||   ||||    ||    ||  |   | |   | | |    |    | || ||  ||   | | || || |||||| | |  | ||  | |||    |||| | | |  ||   || ||||||||||| |||||||||||||||||| | |||||||||||| |  |||| ||| 
-----------------gtagggcagtatgatcgcttatttatcataggtcttttttgacgtggttcacgt-cgtgcttctcttttat------cttgcatctttgtgcacaatgatgtaactc--ctcagacgcagta-gacggacctgacgtctgtgaaa--tttgctatgatgtgctgcagAAACGTCTGCTTGTGGATGTACAAGAGCAGGTGGAGCAGCTTCTTGCAGTTGTCTTTGAAAATTACAAGTCCCTTGATGAGAATTCTTCATCTGGCTTGG
















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: 18 (upstream exon), 58 (downstream exon)
Score: 1

GAATGTTGCAACACCAACAAAAGATTGCTTGGAACTTGCATATGAACTGCTTCTCCCTGTAATGAAAGCACGTGATGATAGGACTTTGACGAGACAAGAGgtaatatgtt ... tttgttgcagAGAAGCATACTATTAGATTGCGAAGATCGGATCAAGAGTCTCCTTGCAGTTGTGTTTGAAAATTACAAGTCCTTGGATGAGAATTCTCCTACTGGTTTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caataaaatgtaaagaataaaataattatggaaacttattttttatttgttgcagAGAAGCATACTATTAGATTGCGAAGATCGGATCAAGAGTCTCCTTGCAGTTGTGTTTGAAAATTACAAGTCCTTGGATGAGAATTCTCCTACTGGTTTGT
                                  cttattttttattt  CT-rich tract
          taaagaataaaataat  TA-rich tract