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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctattaatagtttgtttcatttcaccacattttcatggcatacactaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtattttttgtatgatatggcattgtccaaattgtacagCATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGCCTGATATCTTTAG

Basic information

species Oryza sativa
transcript LOC_Os07g07560.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 8
gtaagctattaatagtttgtttcatttcac-cacattttcatggcata-cactaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtattttttgtatgatatggcattgtccaaattgtacagCATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGCCTGATATCTTTAG
||| ||  ||   |  | ||||   |  |   |  ||   ||  |||| ||||     |    |   |   ||||||   |  || | | | ||         |||      |||   ||  || |||| |||||||    |  ||||||||||||||||| || ||||  |||      || || |||||||||||||| ||| ||||||||||||||||
gtatgcatttgtcaaatagtttttatctatgtattttactattccatatcactgtagtttctttgaaactatttatattttcttagtgctattttcccacttgcctcccccctttgttgttgttgttgt-tgatatg-tggtacccaaattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G082099_T01 (Zea mays), 3'ss of exon 2
gtaagctattaatagtttgtttcatttcaccacattttcatggcatac-actaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtattttttgta--tgatatggcattgtccaaattgtacagCATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGCCTGATATCTTTAG
||| ||  ||   | ||| ||| ||   |     ||   ||  ||| | ||      |    | | |  ||| ||| | ||     ||  | |||| ||  ||| ||||  |  |   | ||| ||||   |||||||       | |||||||||| |||| || ||||| |||      || || |||||||||||||| ||| ||||||||||||||||
gtatgcatttgtcaattt-ttttatccaagtgt-ttactattccatgccacctttgttt--ctttgaaacttcatagattt-----tcttagtgttattttcccaattatctcccccttctttgttgttgttgatatgtggcacccaaaattgtacaaCATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 8
gtaagctattaatagtttgtttcatttcaccacattttcatggcatac-actaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtatttt-ttgta--tgatatggcattgtccaaattgtacagCATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGCCTGATATCTTTAG
||| ||  ||   | ||| ||| ||   |     ||   ||  ||| | ||      |    | | |  ||| ||| | ||    |   | |  |  ||  ||| ||||  || |   |  ||| ||||   |||||||       | ||||||||||||||| || ||||| |||      || || |||||||||||||| ||| ||||||||||||||||
gtatgcatttgtcaattttttttatccaagtgt-ttactattccatgccacctttgttt--ctttgaaacttcatagattt----tcttagtgttatttttcccaattatcttcccccttctttgttgttgttgatatgtggcacccaaaattgtacagCATCCAAGTGGAGAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 3
gtaagctattaatagtttgtttcatttcaccacattttcatggcatac-actaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtatttt-ttgta--tgatatggcattgtccaaattgtacagCATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGCCTGATATCTTTAG
||| ||  ||   | ||| ||| ||   |     ||   ||  ||| | ||      |    | | |  ||| ||| | ||     ||  | |||| ||  ||| ||||  |  |   |  ||| ||||   |||||||       | |||||||||| |||| || ||||| |||      ||  | |||||||||||||| ||| ||||||||||||||||
gtatgcatttgtcaattt-ttttatccaagtgt-ttactattccatgccacctttgttt--ctttgaaacttcatagattt-----tcttagtgttattttcccaattatctccccccttctttgttgttgttgatatgtggcacccaaaattgtacaaCATCCAAGTGGAGAGAGAATAATGGTTATCATGTTGATTATGATCAACGGCCTGATATCTTTAG

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|58659496|gb|CK048176.1|CK048176
EST:     GCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAG                         CATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGC
genomic: GCCTGGATCACCTGACGAGAAGAAGCTTTATCTTATTGATCTTGGTTTAGgtaagctatt ... aattgtacagCATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctattagttttcaagtattttttgtatgatatggcattgtccaaattgtacagCATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGCCTGATATCTTTAG
                 tattttttgtatgata  TA-rich tract