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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaagaagtttgatgtttttctaatggccaggccatcttgttttcttttcctgcttgttgcccagttgggttggcatatttatttttcatcttatttcatgatagtagctcagtgttctgattaacttggccttatttttttagAGCTTCATTATTGCAATTTGTGCCATTGTGATGGCCACATTTTCTACTGGAATCGACACCAGATCCTTCCAA

Basic information

species Oryza sativa
transcript LOC_Os04g42720.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g42720.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G018756_T02 (Zea mays), 3'ss of exon 8
gtaagtaagaagtttgatgtttttctaatggccaggccatcttgttttcttttcctgcttgttgcccagttgggttggcatatttatttttcatcttatttcatgatagtagctcagtgttctgattaacttggccttatttttttagAGCTTCATTATTGCAATTTGTGCCATTGTGATGGCCACATTTTCTACTGGAATCGACACCAGATCCTTCCAA
                                                                   |  |    |  || |  | ||||  ||    ||     || |  | | |     |||||| |    |   |  |||| |||||||||||||| ||||||||| ||||||| |||||||| |||||||||||||||||||||| ||||||||| 
-----------------------------------------------------------------gtaagtaaaatatcagagctcttttgaat--agttctgccattgatgttaa-----ctgattga---agttgtgcttttctagAGCTTCATTATCGCAATTTGTTCCATTGTAATGGCCACGTTTTCTACTGGAATCGACACCAAATCCTTCCAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86414878|gb|CI069281.1|CI069281
EST:     CAATGATGGTGATTGGGCTACCATCGTT                         AGCTTCATTATTGCAATTTGTGCCATTGTGATGGCCACATTTTCTACTGGA
genomic: CAATGATGGTGATTGGGCTACCATTGTTgtaagtaaga ... atttttttagAGCTTCATTATTGCAATTTGTGCCATTGTGATGGCCACATTTTCTACTGGA
EST: gi|86251365|gb|CI055498.1|CI055498
EST:     GCCATACTCGGCTGATATTTGCCAATGATGGTGATTGGGCTACCATTGTT                         AGCTTCATTATTGCAATTTGTGCCATTGTGATGGCCACATTTTCTACTGGA
genomic: GCCATACTCGGCTGATATTTGCCAATGATGGTGATTGGGCTACCATTGTTgtaagtaaga ... atttttttagAGCTTCATTATTGCAATTTGTGCCATTGTGATGGCCACATTTTCTACTGGA

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: 9 (upstream exon), 25 (downstream exon)
Score: 1

CGAACCACAAACTGGAAAGTGCCATACTCGGCTGATATTTGCCAATGATGGTGATTGGGCTACCATTGTTgtaagtaaga ... atttttttagAGCTTCATTATTGCAATTTGTGCCATTGTGATGGCCACATTTTCTACTGGAATCGACACCAGATCCTTCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttatttcatgatagtagctcagtgttctgattaacttggccttatttttttagAGCTTCATTATTGCAATTTGTGCCATTGTGATGGCCACATTTTCTACTGGAATCGACACCAGATCCTTCCAA
                              gattaac  putative branch site (score: 1)
                                         ccttattttttt  putative PPT
                                           ttattttttta  TA-rich tract