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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatttcaacctttcatctcatacacgatcgattttgtattactttattactgcttgtttactgttggtgaggctggtgctacagtgtaaacctttagtgatcttttcaattaccttttctgctgtatcatatattggatactatctgacgtgagctactttgatcagTGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g56490.1
intron # 29
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:     AAGTGCGTATTCAGAAGAAACTTCTGGTTTCTGATGAGCAGTTTGCGAAG                         TGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAA
genomic: AAGTGCGTATTCAGAAGAAACTTCTGGTTTCTGATGAGCAGTTTGCGAAGgtaattattt ... ctttgatcagTGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAA
EST: gi|38483147|gb|CF966949.1|CF966949
EST:     ACGTGCGTATTCAGAAGAAACTTCTGGTTTCTGATGAGCAGTTTGCGAAG                         TGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAA
genomic: AAGTGCGTATTCAGAAGAAACTTCTGGTTTCTGATGAGCAGTTTGCGAAGgtaattattt ... ctttgatcagTGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAA
EST: gi|88324991|gb|CI645005.1|CI645005
EST:     AAGTGCGTATTCAGAAGAAACTTCTGGTTTCTGATGAGCAGTTTGCGAAG                         TGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAA
genomic: AAGTGCGTATTCAGAAGAAACTTCTGGTTTCTGATGAGCAGTTTGCGAAGgtaattattt ... ctttgatcagTGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAA
EST: gi|218495798|gb|FG954256.1|FG954256
EST:     AAGTGCGTATTCAGAAGAAACTTCTGGTTTCTGATGAGCAGTTTGCGAAG                         TGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAA
genomic: AAGTGCGTATTCAGAAGAAACTTCTGGTTTCTGATGAGCAGTTTGCGAAGgtaattattt ... ctttgatcagTGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAA
EST: gi|33810373|gb|CF331077.1|CF331077
EST:     AAGTGCGTATTCAGAAGAAACTTCTGGTTTCTGATGAGCAGTTTGCGAAG                         TGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAA
genomic: AAGTGCGTATTCAGAAGAAACTTCTGGTTTCTGATGAGCAGTTTGCGAAGgtaattattt ... ctttgatcagTGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAA
EST: gi|86887682|gb|CI311889.1|CI311889
EST:     GTATTCCAGAAGAAACTTTTTGGTTTTTAATGAGCAGTTTGCNAAAG                         TGNAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGGTGAATACTTTC
genomic: GTATT-CAGAAGAAAC-TTCTGGTTTCTGATGAGCAGTTTGC-GAAGgtaattattt ... ctttgatcagTGGAAATTTGCTTATATTGCTCACAATCGCCTGGCT-GGTGAATACTTTC

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: 71 (upstream exon), 73 (downstream exon)
Score: 11

AGAACCTTTCTTCTTTCTTATCCGTGATGGTGAGACATTATCAGATATCAAAGTGCGTATTCAGAAGAAACTTCTGGTTTCTGATGAGCAGTTTGCGAAGgtaattattt ... ctttgatcagTGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttctgctgtatcatatattggatactatctgacgtgagctactttgatcagTGGAAATTTGCTTATATTGCTCACAATCGCCTGGCTGGTGAATACTTTCAAGATTCAGATATCGTATTGAGCCGATTCCAG
                              atctgac  putative branch site (score: 11)
                                          ctacttt  putative PPT
            tatcatatatt  TA-rich tract