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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgatcctttatatctccatgatcctcacgcacaagaacacaagcatactctactcttaatgctaatacaatatcggattctgttgttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT

Basic information

species Oryza sativa
transcript LOC_Os01g59850.1
intron # 11
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|88962987|gb|CI025473.1|CI025473
EST:     AATTCTAACATGCCTTATATTTCCTCTGGGCCACAGG                         GAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
genomic: AATTCTAACATGCCTTATATTTCCTCTGGGCCACAGGgtatctgatc ... gttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
EST: gi|29628793|gb|CB633804.1|CB633804
EST:     ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGG                         GAGGATTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
genomic: ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGGgtatctgatc ... gttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
EST: gi|88231471|gb|CI231320.1|CI231320
EST:     ATGGATACCTCATAATTCTAACATGCCTTATATCTCCTCTGGGCCACAGG                         GAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
genomic: ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGGgtatctgatc ... gttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
EST: gi|32947805|gb|BP184377.1|BP184377
EST:     ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGG                         GAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
genomic: ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGGgtatctgatc ... gttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
EST: gi|29671473|gb|CB667748.1|CB667748
EST:     ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGG                         GAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
genomic: ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGGgtatctgatc ... gttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
EST: gi|12623253|gb|AU173466.1|AU173466
EST:     ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGG                         GAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
genomic: ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGGgtatctgatc ... gttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
EST: gi|86874259|gb|CI335871.1|CI335871
EST:     ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGG                         GAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
genomic: ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGGgtatctgatc ... gttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
EST: gi|29669999|gb|CB666274.1|CB666274
EST:     ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGG                         GAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
genomic: ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGGgtatctgatc ... gttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
EST: gi|29626174|gb|CB631185.1|CB631185
EST:     ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGG                         GAGGATTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
genomic: ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGGgtatctgatc ... gttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
EST: gi|18386972|gb|BM420170.1|BM420170
EST:     ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGG                         GAGGATTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
genomic: ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGGgtatctgatc ... gttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
EST: gi|29624490|gb|CB629501.1|CB629501
EST:     ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGG                         GAGGATTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
genomic: ATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGGgtatctgatc ... gttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT

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), 46 (downstream exon)
Score: 29

ACGTTGCCAAATCCCCATGTCAATACAGATTATTCCAACTTGACTGAGTCATGGATACCTCATAATTCTAACATGCCTTATATTTCCTCTGGGCCACAGGgtatctgatc ... gttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagcatactctactcttaatgctaatacaatatcggattctgttgttgtttcagGAGGGTTATCATACATGGCAACACAAGTACAAGACTCCCTCATGCT
                    tgctaat  putative branch site (score: 29)
                                              ttgtttc  putative PPT
                       taatacaatat  TA-rich tract