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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgctaatgttgttttgtgggttgttaatttctatactaattcaatccagttagtaatctccttgttttaaccacttctgatgcattttccctgtagGATGATGCCCATATTTTTTGCAGAGAAAGCCAA

Basic information

species Oryza sativa
transcript LOC_Os08g19850.1
intron # 12
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|2311510|gb|C27665.1|C27665
EST:     GCACTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAG                         GATGATGCCCATATTTTTTGCAGAGAAAGCCAA
genomic: GCACTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaatgctaa ... ttccctgtagGATGATGCCCATATTTTTTGCAGAGAAAGCCAA
EST: gi|29626606|gb|CB631617.1|CB631617
EST:     AGCTTAGTGGTGCACTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAG                         GATGATGCCCATATTTTTTGCAGAGAAAGCCAA
genomic: AGCTTAGTGGTGCACTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaatgctaa ... ttccctgtagGATGATGCCCATATTTTTTGCAGAGAAAGCCAA
EST: gi|88376802|gb|CI639127.1|CI639127
EST:     AGCTTAGTGGTGCACTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAG                         GATGATGCCCATANNNNNNNGCAGAGAAAGCCAA
genomic: AGCTTAGTGGTGCACTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaatgctaa ... ttccctgtagGATGATGCCCATATTTTTT-GCAGAGAAAGCCAA
EST: gi|29686166|gb|CB682441.1|CB682441
EST:     AGCTTAGTGGTGCACTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAG                         GATGATGCCCATATTTTTTGCAGAGAAAGCCAA
genomic: AGCTTAGTGGTGCACTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaatgctaa ... ttccctgtagGATGATGCCCATATTTTTTGCAGAGAAAGCCAA

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: 75 (upstream exon), 71 (downstream exon)
Score: 34

AATTGCCTCTCCGGATGGCTGATTTTGGAGTCCTTCACAGGAATGAGCTTAGTGGTGCACTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaatgctaa ... ttccctgtagGATGATGCCCATATTTTTTGCAGAGAAAGCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatccagttagtaatctccttgttttaaccacttctgatgcattttccctgtagGATGATGCCCATATTTTTTGCAGAGAAAGCCAA
                                         cattttccct  CT-rich tract
                    ttgttttaa  TA-rich tract