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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcatagcttttcaatgttacgcataccgtctctttattatcatatgatagaacaatgaccttttttatgtcttgcgttgccttctgattgtttttggtgatttcatgcttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTGAGTGCACAGGCCCATCGTCAGGAATTGATACAGGATCTTTTTAAAGTAT

Basic information

species Oryza sativa
transcript LOC_Os02g45070.2
intron # 15
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|58681347|gb|CK070034.1|CK070034
EST:     ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCT                         GTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
genomic: ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCTgtaagtgcat ... cttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
EST: gi|38471881|gb|CF956012.1|CF956012
EST:     TGTTACACATCCCCATCCTGNGAGAAGATTCTAGCCCTTCCATTGCAGCT                         GTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
genomic: TGTTACACATCCCCATCCTG-GAGAAGATTCTAGCCCTTCCATTGCAGCTgtaagtgcat ... cttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
EST: gi|58666415|gb|CK055101.1|CK055101
EST:     ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCT                         GTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
genomic: ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCTgtaagtgcat ... cttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
EST: gi|33801495|gb|CF326620.1|CF326620
EST:     ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCT                         GTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
genomic: ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCTgtaagtgcat ... cttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
EST: gi|58652663|gb|CK041343.1|CK041343
EST:     ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCT                         GTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
genomic: ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCTgtaagtgcat ... cttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
EST: gi|14571449|gb|BI118817.1|BI118817
EST:     ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCT                         GTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
genomic: ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCTgtaagtgcat ... cttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
EST: gi|58674483|gb|CK063170.1|CK063170
EST:     ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCT                         GTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
genomic: ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCTgtaagtgcat ... cttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
EST: gi|58681274|gb|CK069961.1|CK069961
EST:     ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCT                         GTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
genomic: ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCTgtaagtgcat ... cttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
EST: gi|33797058|gb|CF324395.1|CF324395
EST:     ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCT                         GTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
genomic: ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCTgtaagtgcat ... cttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
EST: gi|58653440|gb|CK042120.1|CK042120
EST:     ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCT                         GTTGTTGCTTCTCCAGACTGGCCTGAGGTCACCAAATATGCCGGATT
genomic: ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCTgtaagtgcat ... cttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATT
EST: gi|14571456|gb|BI118824.1|BI118824
EST:     ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCT                         GTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
genomic: ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCTgtaagtgcat ... cttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
EST: gi|11544371|gb|BF475189.1|BF475189
EST:     ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCT                         GTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG
genomic: ATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCTgtaagtgcat ... cttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTG

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: 52

AAGGAGGATTCCCCTTGTGAGTGATAGGCCAACGATCATTTTTGGTGCTGATGTTACACATCCCCATCCTGGAGAAGATTCTAGCCCTTCCATTGCAGCTgtaagtgcat ... cttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTGAGTGCACAGGCCCATCGTCAGGAATTGATACAGGATCTTTTTAAAGTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatgtcttgcgttgccttctgattgtttttggtgatttcatgcttcatgcagGTTGTTGCTTCTCAAGACTGGCCTGAGGTCACCAAATATGCCGGATTAGTGAGTGCACAGGCCCATCGTCAGGAATTGATACAGGATCTTTTTAAAGTAT
                   ttctgat  putative branch site (score: 52)
                        attgttttt  TA-rich tract