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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttaaattctcttttaagagttgagtcggattattctcaaataatttttttctgccttgtttatttaatatagAAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAG

Basic information

species Oryza sativa
transcript LOC_Os01g56490.1
intron # 30
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|58662695|gb|CK051381.1|CK051381
EST:     TGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAG                         AAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGAC
genomic: TGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAGgtgggttaaa ... tttaatatagAAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGAC
EST: gi|88324991|gb|CI645005.1|CI645005
EST:     TGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAG                         AAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGAC
genomic: TGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAGgtgggttaaa ... tttaatatagAAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGAC
EST: gi|88465709|gb|CI524659.1|CI524659
EST:     TGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAG                         AAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGAC
genomic: TGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAGgtgggttaaa ... tttaatatagAAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGAC
EST: gi|33810375|gb|CF331078.1|CF331078
EST:     TGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAG                         AAAGATTTTTATGGACCATGGGAACAATGCNTAGGACTTGAGCACTCAGAC
genomic: TGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAGgtgggttaaa ... tttaatatagAAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGAC
EST: gi|218495798|gb|FG954256.1|FG954256
EST:     TGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAG                         AAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGAC
genomic: TGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAGgtgggttaaa ... tttaatatagAAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGAC
EST: gi|33810373|gb|CF331077.1|CF331077
EST:     TGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAG                         AAAGATTTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGAC
genomic: TGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAGgtgggttaaa ... tttaatatagAAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGAC
EST: gi|86887682|gb|CI311889.1|CI311889
EST:     GGCTGGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAG                         AAAGATGTTTATGGACCATGGGAACAATGCTTAGGACTTGAGCACTCAGAC
genomic: GGCT-GGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAGgtgggttaaa ... tttaatatagAAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGAC
EST: gi|9865065|gb|AU100815.1|AU100815
EST:     GGCTGGTGAATACTTTCAAAGATTCAGATATCGTATTGANCCGATTCCAG                         AAAGATGTTTATGGACCATGGGNACAATGCCTAGGACTTGAGCACTCAGNC
genomic: GGCTGGTGAATACTTTC-AAGATTCAGATATCGTATTGAGCCGATTCCAGgtgggttaaa ... tttaatatagAAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGAC

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: 58 (upstream exon), 50 (downstream exon)
Score: 6

TGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAGgtgggttaaa ... tttaatatagAAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgagtcggattattctcaaataatttttttctgccttgtttatttaatatagAAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAG
                                            atttaat  putative branch site (score: 6)
                          tttttttctgccttgt  CT-rich tract
                    aaataatttttttctg  TA-rich tract