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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcacaccattcaatagtgtaaatcatgaaattgacacatattctgcaaggtgcaactcttgtattgacacataatatgctcttctacttttggttccagGTATATTTGTGGCACTTGCGCTGCGTTTTGATGTCTCAAGAGGAATTAAGAACCGCTATTTTAATAGTGCATTTTTGGGTTATACCGTGGGTCTGACTGT

Basic information

species Oryza sativa
transcript LOC_Os05g36070.2
intron # 9
splice site 3'
intron type U2

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|88244093|gb|CI243215.1|CI243215
EST:     TTCTCTATGCTTGGCCTTGGTGACATTGTAATACCTG                         GTATATTTGTGGCACTTGCGCTGCGTTTCGATGTCTCAAGAGGAATTAAGA
genomic: TTCTCTATGCTTGGCCTTGGTGACATTGTAATACCTGgttagtaata ... ttggttccagGTATATTTGTGGCACTTGCGCTGCGTTTTGATGTCTCAAGAGGAATTAAGA
EST: gi|8859158|gb|AU096476.1|AU096476
EST:     TGCTGCACG-CCGTTCTCTATGCTTGGCCTTGGTGACATTGTAANACCTG                         GTATATTTGTGGCACTTGCGCTGCGTTTTGATGTCTCAAGAGGAATTAAGA
genomic: TGCTGCACGCCCGTTCTCTATGCTTGGCCTTGGTGACATTGTAATACCTGgttagtaata ... ttggttccagGTATATTTGTGGCACTTGCGCTGCGTTTTGATGTCTCAAGAGGAATTAAGA
EST: gi|29628338|gb|CB633349.1|CB633349
EST:     TGCTGCACGCCCGTTCTCTATGCTTGGCCTTGGTGACATTGTAATACCTG                         GTATATTTGTGGCACTTGCGCTGCGTTTTGATGTCTCAAGAGGAATTAAGA
genomic: TGCTGCACGCCCGTTCTCTATGCTTGGCCTTGGTGACATTGTAATACCTGgttagtaata ... ttggttccagGTATATTTGTGGCACTTGCGCTGCGTTTTGATGTCTCAAGAGGAATTAAGA
EST: gi|29628337|gb|CB633348.1|CB633348
EST:     TGCTGCACGCCCGTTCTCTATGCTTGGCCTTGGTGACATTGTAATACCTG                         GTATATTTGTGGCACTTGCGCTGCGTTTTGATGTCTCAAGAGGAATTAAGA
genomic: TGCTGCACGCCCGTTCTCTATGCTTGGCCTTGGTGACATTGTAATACCTGgttagtaata ... ttggttccagGTATATTTGTGGCACTTGCGCTGCGTTTTGATGTCTCAAGAGGAATTAAGA
EST: gi|88840958|gb|CI000920.1|CI000920
EST:     CATTGTAATACCTG                         GTATATTTGTGGCACTTGCGCTGCGTTTTGATGTCTCAAGAGGAATTAAGA
genomic: CATTGTAATACCTGgttagtaata ... ttggttccagGTATATTTGTGGCACTTGCGCTGCGTTTTGATGTCTCAAGAGGAATTAAGA

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: 70 (upstream exon), 51 (downstream exon)
Score: 39

CTTCTATTTCCTACAGGTGATGCTGCACGCCCGTTCTCTATGCTTGGCCTTGGTGACATTGTAATACCTGgttagtaata ... ttggttccagGTATATTTGTGGCACTTGCGCTGCGTTTTGATGTCTCAAGAGGAATTAAGAACCGCTATTTTAATAGTGCATTTTTGGGTTATACCGTGGGTCTGACTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaggtgcaactcttgtattgacacataatatgctcttctacttttggttccagGTATATTTGTGGCACTTGCGCTGCGTTTTGATGTCTCAAGAGGAATTAAGAACCGCTATTTTAATAGTGCATTTTTGGGTTATACCGTGGGTCTGACTGT
                 tattgac  putative branch site (score: 39)
                                tgctcttctactttt  putative PPT
                        acataatat  TA-rich tract