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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaggccactatgtcaccattgtcattttcaaggtgtattgtttcaaaagttgatgcaaccaggaaatgcttagcgagtcctggacactgatgcaagttgatgcatgttctcttcagtctgatatttggttttgcataatgttcccagAGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATGATCAACCATTATTTCCGAGCATCGATCTCTGGGATTGGGATATGGTCAA

Basic information

species Oryza sativa
transcript LOC_Os01g07540.1
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|218485966|gb|FG956970.1|FG956970
EST:     TGAATTGCAAAATGAGAATTCGACAGCCGTGCATGAATCTCTGAGTGAAG                         AGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG
genomic: TGAATTGCAAAATGAGAATTCGACAGCCGTGCATGAATCTCTGAGTGAAGgtgagaggcc ... atgttcccagAGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG
EST: gi|95101518|gb|CI697037.1|CI697037
EST:     ATTCGACAGCCGTGCATGAATCTCTGAGTGAAG                         AGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG
genomic: ATTCGACAGCCGTGCATGAATCTCTGAGTGAAGgtgagaggcc ... atgttcccagAGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG
EST: gi|88581732|gb|CI698935.1|CI698935
EST:     ATTCGACAGCCGTGCATGAATCTCTGAGTGAAG                         AGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG
genomic: ATTCGACAGCCGTGCATGAATCTCTGAGTGAAGgtgagaggcc ... atgttcccagAGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG
EST: gi|88442766|gb|CI693772.1|CI693772
EST:     ATTCGACAGCCGTGCATGAATCTCTGAGTGAAG                         AGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG
genomic: ATTCGACAGCCGTGCATGAATCTCTGAGTGAAGgtgagaggcc ... atgttcccagAGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG
EST: gi|88352861|gb|CI678889.1|CI678889
EST:     ATTCGACAGCCGTGCATGAATCTCTGAGTGAAG                         AGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG
genomic: ATTCGACAGCCGTGCATGAATCTCTGAGTGAAGgtgagaggcc ... atgttcccagAGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG
EST: gi|88579450|gb|CI688438.1|CI688438
EST:     ATTCGACAGCCGTGCATGAATCTCTGAGTGAAG                         AGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG
genomic: ATTCGACAGCCGTGCATGAATCTCTGAGTGAAGgtgagaggcc ... atgttcccagAGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG
EST: gi|27548609|gb|CA766815.2|CA766815
EST:     TGAATTGCAAAATGAGAATTCGACAGCCGTGCATGAATCTCTGAGTGAAG                         AGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG
genomic: TGAATTGCAAAATGAGAATTCGACAGCCGTGCATGAATCTCTGAGTGAAGgtgagaggcc ... atgttcccagAGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATG

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: 59 (upstream exon), 46 (downstream exon)
Score: 4

GAAAATGCACCATCCTCTCCATGTGATGCTTCCTTGCACCAAACAGAAGATGAATTGCAAAATGAGAATTCGACAGCCGTGCATGAATCTCTGAGTGAAGgtgagaggcc ... atgttcccagAGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATGATCAACCATTATTTCCGAGCATCGATCTCTGGGATTGGGATATGGTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagttgatgcatgttctcttcagtctgatatttggttttgcataatgttcccagAGGAAGAGAAATGGCTTGCTCAGTATGGTCAGGTAGAGCAAGAAATTGATGATCAACCATTATTTCCGAGCATCGATCTCTGGGATTGGGATATGGTCAA
                       gtctgat  putative branch site (score: 4)
                                              tgttccc  putative PPT
                          tgatattt  TA-rich tract