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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggccatttctttttatcataaactattagtcacttggagtaactagtgagtatatcatattatctcaaaaaaaaaaatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g01800.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G036206_T01 (Zea mays), 3'ss of exon 6
gtaggccatttctttttatcataaactattagtcacttggagtaactagtgagtatatcatattatctcaaaaaaaaaaatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
||| |   || | |||||||  ||   | || |  |||||       |||| || |||||| | |||| || |         |||||||||||||| |||||||| || ||||||||||||||||| ||||||||||| ||||| || ||||||||||||||||||||||| |||||  | |||||  
gtaagatgtt-cattttatcgaaagagaataattccttgg-------agtgtgtctatcatctcatcttaatagttg----ttttcagGCATTTGACCAGCAGCAGCATGATTTAATTGATGCAGCTTCAAAAGCTTTGTCATACAGGCAAGATATTATTGAGGAAAACATTCGTCTCACGTATGCGT

upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G31880.1 (Glycine max), 3'ss of exon 7
--------------------------------------gtaggccatttctttttatcataaactattagtcacttggagtaactagtgagtatatcatattatctcaaaaaaaaaaatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
                                       || ||   || | | | |   |   |     | | |||    | ||  ||   | || | || || |  || |       ||   |||| ||||||||||||||||| ||  |  | ||||| ||||||||||||||||||||  ||||||| || ||||| ||||| || |||||  |||||||| 
gtatgcatgaaattttgtcaaagtctttgtgaaattccttaagcatcttttatgttttgcacttttccttttatttgattgagcttctgctcaaat-aaataatttgtaatattg----ctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT

upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G35770.1 (Glycine max), 3'ss of exon 8
--------------------------------------gtaggccatttctttttatcataaactattagtcacttggagtaactagtgagtatatcatattatctcaaaaaaaaaaatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
                                       || ||   || | | | |   |   |       | ||||   | ||  ||   | || | || || |  || |       ||   |||| ||||||||||||||||| ||  |  | ||||| ||||||||||||||||||||  ||||||| || ||||| ||||| || |||||  |||||||| 
gtatgcatgaaattttgttgaaatctttgtgaaattccttaagcatcttttgtgttttgcatttttccttatatttggttgagcttctgctcaaat-aaataatttgtaatattg----ctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT

upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G08440.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaggccatttctttt---tatcataaactattagtcacttgga---gtaactagtgagtatatcatattatctcaa------aaaaaaaaatctttc--------------agGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
||  ||  ||  ||||   ||| | ||| |||  || ||||      || || | | |   |  | |||| | | ||      |      ||| | ||              |||||||||| || || ||||||||  |  ||||||| |||||||||||| | || || |||||||| || ||||||||||| || || ||  |||||||  
gttagcttttctttttatctattacaaaatatgtgtaactttatcttgtgacgaattatagttacttattctgttaaccacttagggggtaatttatctttcttgttgtgacagGCATTTGACCAACAACAACAAGACCTTGTTGATGCTGCATCAAAAGCTCTTTCTTACAGACAAGAGATCATTGAGGAAAATATACGCCTAACATATGCCT

upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G23490.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaggccatttctttttatca-taaactattagtcacttggagtaactagtgagtatatcatattatctcaaaaa--aaaaaatcttt-----------cagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
||||||| || |||||| | | | | || ||     | |   |||   | ||  | ||   || |   |   ||    ||| ||  ||           |||||||||||||| |||||||||||| |  |||||||  ||||||||||| | || || |||||||| || ||||| ||||| || || ||  |||||||  
gtaggcctttccttttttttacttatctgttttattcatctcgtattaaatgtatttaatttaattgtttggaagctgaaagattgttgctgttgtaaccagGCATTTGATCAACAGCAACAAGATCTTGTTGATGCTTCATCAAAAGCTCTCTCTTACAGACAAGAGATAATTGAAGAAAATATACGCCTAACATATGCCT

upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 6
gtaggccatttct----ttttatcataaactattagtcacttggagtaact----agtgagtatatcatattatctcaaaaaaaaaaatctttc----agGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
 ||     || ||    |||| | | || | |  |    |||   ||   |    || | ||  ||   |   | |            ||||      |||| |||||||| || ||||||||| |  ||||||| || ||||||||| | ||||| |||||||| ||||||||||||||||| |||||  |||||||| 
ttatatttttcctcaaattttctgagaaccaaacatagcctttatgttttttttgagggggttcatggaaagtttttgtccttcttcttcttcttgctagGCTTTTGATCAACAACAACAAGATCTTGTTGATGCGGCCTCAAAAGCTCTTTCATACAGACAAGACATTATTGAGGAAAACATTCGTCTCTCATATGCAT

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|29674957|gb|CB671232.1|CB671232
EST:     TACTCGATGATAAATATATGTTGGAAAAGCGCATTGCTCAAATGCGGATG                         GCATTTGATCAGCAG
genomic: TACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATGgtaggccatt ... aatctttcagGCATTTGATCAGCAG
EST: gi|32947856|gb|BP184428.1|BP184428
EST:     TACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATG                         GCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTA
genomic: TACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATGgtaggccatt ... aatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTA
EST: gi|58673928|gb|CK062614.1|CK062614
EST:     TACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATG                         GCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTA
genomic: TACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATGgtaggccatt ... aatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTA
EST: gi|29628865|gb|CB633876.1|CB633876
EST:     TACTCGATGATATATATATGTTGGAGAGGCGCATTGCTCAAATGCGGATG                         GCATTTGATCAGC
genomic: TACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATGgtaggccatt ... aatctttcagGCATTTGATCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttggagtaactagtgagtatatcatattatctcaaaaaaaaaaatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
      gagtaac  putative branch site (score: 2)
                                               tctttc  putative PPT
                  agtatatcatattatc  TA-rich tract