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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcatccttcatgattgaagatcatgaaattctcacatatttctgcaagcagcaactcttctattaacaaataatactcacttctacttttgtttccagGTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGAACCGCTACTTCAATAGTGCATTTTTGGGTTATACGGTGGGTTTGACCGT

Basic information

species Oryza sativa
transcript LOC_Os02g02530.2
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|86436738|gb|CI118460.1|CI118460
EST:     TGCTGCACGCCCATTCTCTATGCTTGGGCTTGGTGACATTGTGATACCTG                         GTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGA
genomic: TGCTGCACGCCCATTCTCTATGCTTGGGCTTGGTGACATTGTGATACCTGgttagtaatg ... ttgtttccagGTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGA
EST: gi|58684751|gb|CK073438.1|CK073438
EST:     TGCTGCACGCCCATTCTCTATGCTTGGGCTTGGTGACATTGTGATACCTG                         GTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGA
genomic: TGCTGCACGCCCATTCTCTATGCTTGGGCTTGGTGACATTGTGATACCTGgttagtaatg ... ttgtttccagGTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGA
EST: gi|3768652|gb|AU032679.1|AU032679
EST:     ACATTGTGATACCTG                         GTATATTTGTTGCGCTAGCNCTGCGGTTTGATGTCTCANGNGGANTTTAAG
genomic: ACATTGTGATACCTGgttagtaatg ... ttgtttccagGTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGA-ATTAAG
EST: gi|3764135|gb|AU030635.1|AU030635
EST:     CTTGGGCTTGGTGACATTGTGATACCTG                         GTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGA
genomic: CTTGGGCTTGGTGACATTGTGATACCTGgttagtaatg ... ttgtttccagGTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGA
EST: gi|29629872|gb|CB634881.1|CB634881
EST:     TGCTGCACGCCCATTCTCTATGCTTGGGCTTGGTGACATTGTGATACCTG                         GTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGA
genomic: TGCTGCACGCCCATTCTCTATGCTTGGGCTTGGTGACATTGTGATACCTGgttagtaatg ... ttgtttccagGTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGA
EST: gi|87031167|gb|CI259747.1|CI259747
EST:     TGCTGCACGCCCATTCTCTATGCTTGGGCTTGGTGACATTGTGATACCTG                         GTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGA
genomic: TGCTGCACGCCCATTCTCTATGCTTGGGCTTGGTGACATTGTGATACCTGgttagtaatg ... ttgtttccagGTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGA
EST: gi|29660567|gb|CB656842.1|CB656842
EST:     TGCTGCACGCCCATTCTCTATGCTTGGGCTTGGTGACATTGTGATACCTG                         GTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGA
genomic: TGCTGCACGCCCATTCTCTATGCTTGGGCTTGGTGACATTGTGATACCTGgttagtaatg ... ttgtttccagGTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGA

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), 73 (downstream exon)
Score: 42

CTTCTATTTCCAACAGGAGATGCTGCACGCCCATTCTCTATGCTTGGGCTTGGTGACATTGTGATACCTGgttagtaatg ... ttgtttccagGTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGAACCGCTACTTCAATAGTGCATTTTTGGGTTATACGGTGGGTTTGACCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaagcagcaactcttctattaacaaataatactcacttctacttttgtttccagGTATATTTGTTGCGCTAGCACTGCGGTTTGATGTCTCAAGAGGAATTAAGAACCGCTACTTCAATAGTGCATTTTTGGGTTATACGGTGGGTTTGACCGT
                              tactcac  putative branch site (score: 42)
                                ctcacttctacttttg  CT-rich tract
              ttctattaacaaataa  TA-rich tract