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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatcagatttttttgttgttttgtacaggaaagtcgaagcactttgtacttgatcttaccttttgtgaagttctttttttcatcttcttgctatccaatggtacagcctatacagtgtaccatgtgctaacactagacatggttcttgtttactgacaagcttatctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCT

Basic information

species Oryza sativa
transcript LOC_Os01g56630.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G079389_T01 (Zea mays), 3'ss of exon 10
gtacgtatcagatttttttgttgttttgtacaggaaagtcgaagcactttgtacttgatcttaccttttgtgaagttctttttttcatcttcttgctatccaatggtacagcctatacagtgtaccatgtgctaacactagacatggttcttgtttactgacaagcttatctac---tatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCT
||| |||||||| | ||| |||||| ||||||||||||| |||  |||  ||  ||| ||| |||  ||| ||||||   ||||  |  | | | ||||    || |||||  | ||   ||   | ||    |  | | |   |  |   |||||| ||| |||||| | |||   |  |||||||||||||||| |||||||| ||||| ||| ||||||| ||||| ||||||||||||||||||||||| |||||||| |||||||| ||||| ||||
gtaggtatcagaatcttt-gttgttctgtacaggaaagttgaa--actaggtctttggtct-accaattg-gaagtttccttttgaacttccctactatttgctgctacagtttttattttg---cgtgcaacactatttgtagtactaactgtttaatgataagcttgtatacacttgcagGATGTCTACCTTCACACAAACTGTCTTGCTATTTTAGCAAACATGGCTCCTCATGTGCATAGGCTGAGTGCTTATGCATCACAAAGGCTAGTTAGTCTCT

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G078576_T03 (Zea mays), 3'ss of exon 9
gtacgtatcagatttttttgttgttttgtacaggaaagtcgaagcactttgtacttgatcttaccttttgtgaagttctttttttcatcttcttgctatccaatggtacagcctatacagtgtaccatgtgctaacactagacatggttcttgtttactgacaagcttatctac---tatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCT
||| |||||||| | ||  |||||||||||||| ||| | |||  |||  || | |||||  |||  ||| |||  |   ||||  |  ||  ||||||  | || || ||  | ||| |||| | |  |      | | |   || |   |||||| ||| ||| |||| |||   |  |||||||||||||||| |||||||| ||||||||| ||||||||||||| || |||||||||||||||||||| |||||||| |||||||| ||||| ||||
gtaggtatcagaatcttc-gttgttttgtacag-aaaatagaa--actaggttcctgatc--accaattg-gaaactgccttttgaactttgctgctatttactgctatagtttgtactgtgtgcaacat-----tatttgtagtgctaactgtttaatgataagattatatacacttgcagGATGTCTACCTTCACACAAACTGTCTTGCAATTTTAGCAAATATGGCTCCGCATGTGCATAGGCTGAGTGCTTATGCATCACAAAGGCTAGTTAGTCTCT
















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|58684083|gb|CK072770.1|CK072770
EST:     TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGA                         GATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
genomic: TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGAgtacgtatca ... tctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
EST: gi|58678344|gb|CK067031.1|CK067031
EST:     TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGA                         GATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
genomic: TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGAgtacgtatca ... tctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
EST: gi|29628456|gb|CB633467.1|CB633467
EST:     TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGA                         GATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
genomic: TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGAgtacgtatca ... tctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
EST: gi|58693104|gb|CK081791.1|CK081791
EST:     TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGA                         GATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
genomic: TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGAgtacgtatca ... tctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
EST: gi|29639051|gb|CB644060.1|CB644060
EST:     TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGA                         GATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
genomic: TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGAgtacgtatca ... tctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatgtgctaacactagacatggttcttgtttactgacaagcttatctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCT
                               tactgac  putative branch site (score: 1)
                                         cttatct  putative PPT
                          ttgttta  TA-rich tract