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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtattccccagttcaacttaacctgtttaagctcatcatgtttatgtataccttttctttttctaagttaattgttgagtgtaaaatcaagagatttttatttgtaagtctcgcctatactactgcttattgaatccttttctttctttctttcttttttgaaccagAGAGCGAACCCAATCAGGTGCTGGTGCAG

Basic information

species Oryza sativa
transcript LOC_Os03g03920.3
intron # 4
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|29672914|gb|CB669189.1|CB669189
EST:     TCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCC                         AGAGCGAACCCAATCAGGTGCTGGTGCAG
genomic: TCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCCgtgagtattc ... tttgaaccagAGAGCGAACCCAATCAGGTGCTGGTGCAG
EST: gi|88955489|gb|CI091581.1|CI091581
EST:     TCATTCCAGCAGTCCTGGATGTCACAACTTGGTCAACAACAAGCTGGCCC                         AGAGCGAACCCAATCAGGTGCTGGTGCAG
genomic: TCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCCgtgagtattc ... tttgaaccagAGAGCGAACCCAATCAGGTGCTGGTGCAG
EST: gi|88844161|gb|CI001218.1|CI001218
EST:     TCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCC                         AGAGCGAACCCAATCAGGTGCTGGTGCAG
genomic: TCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCCgtgagtattc ... tttgaaccagAGAGCGAACCCAATCAGGTGCTGGTGCAG
EST: gi|86482742|gb|CI125375.1|CI125375
EST:     TCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCC                         AGAGCGAACCCAATCAGGTGCTGGTGCAG
genomic: TCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCCgtgagtattc ... tttgaaccagAGAGCGAACCCAATCAGGTGCTGGTGCAG
EST: gi|86500583|gb|CI143216.1|CI143216
EST:     TCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCC                         AGAGCGAACCCAATCAGGTGCTGGTGCAG
genomic: TCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCCgtgagtattc ... tttgaaccagAGAGCGAACCCAATCAGGTGCTGGTGCAG
EST: gi|86486868|gb|CI129501.1|CI129501
EST:     CTTGATGTCACAACTTGGTCAACAACAAGCTGGCCC                         AGAGCGAACCCAATCAGGTGCTGGTGCAG
genomic: CTTGATGTCACAACTTGGTCAACAACAAGCTGGCCCgtgagtattc ... tttgaaccagAGAGCGAACCCAATCAGGTGCTGGTGCAG

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: 73 (upstream exon), 75 (downstream exon)
Score: 68

TGGAAATCAGATGGCTTATGATGATTTTTTTGTGTGTATAGCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCCgtgagtattc ... tttgaaccagAGAGCGAACCCAATCAGGTGCTGGTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctatactactgcttattgaatccttttctttctttctttcttttttgaaccagAGAGCGAACCCAATCAGGTGCTGGTGCAG
          ctgcttattgaatcct  CT-rich tract
                                  tttctttctttttt  TA-rich tract