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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtttttaaaatttattcatttgtgattctttttgctcaacaagtttcagtttaataaatatgctgatactccattttttaaccaaatcctccactcagGGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAG

Basic information

species Oryza sativa
transcript LOC_Os11g36070.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g36070.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G135314_T01 (Zea mays), 3'ss of exon 1
-tagttt-ttaaaatttattcatttgtgattctttttgctcaacaagtttcagtttaataaatatgctgatactccattttttaaccaaatcctccactcagGGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAG
 || |   ||  ||    ||| ||| | || ||  |   |   ||  |||||| || | |||||| ||| || ||  ||||||   ||| |       |||||||| ||||||||||||||||||||||||| || |||||||||||| | |||||||||||||||||||||||||| |||||||| ||||| || ||||| 
ctaatccattttaagcatttcttttatcatactagt-attattcatttttcagctttaaaaatatactg-tattcatttttttccgcaattaacatcatcagGGCAGTAGCTAATATGGATATTAAGCTAGATTTTGTTCCACCATGGTTGATCAACTTCATATCAAGGCAACTAATAGGCAGCGGGCATAAGCTGTATCAA

upper sequence: LOC_Os11g36070.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G104449_T02 (Zea mays), 3'ss of exon 8
tagtttttaaaatttattcatttgtgattctttttgctcaacaagtttc--agtttaataaatatgctg-atactccattttttaaccaaatcctccactcagGGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAG
 | ||||| || | | ||| ||| |  |  |  | ||   |    ||||  || ||   |||||| ||| ||      || ||||   ||||||||   ||||||||||||||||||||||||| |||||||| || |||||||||||| | ||||||||||| |||||||||||||| |||||||| ||||| || ||||| 
-atttttttaagtat-ttccttttttttcatgctagcattattcatttcgcagctttcaaaatatactgtattgatttttctttagttaaatcctctg-tcagGGCAATAGCTAATATGGATATCAAGCTAGATTTTGTTCCACCATGGTTGATCAACTTCATGTCAAGGCAACTAATAGGCAGCGGGCATAAGCTGTATCAA

upper sequence: LOC_Os11g36070.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ34640 (Selaginella moellendorffii), 3'ss of exon 7
tagtttttaaaatttattcatttgtgattctttttgctcaacaagtttcagtttaataaatatgctgatactccattttttaaccaaatcctccactcagGGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAG
                                          |  ||  || ||    |   |     |  |     ||| | |  | |  | | |  ||| |  | |  ||||||||||| ||||| ||||| |||||||| ||| | |||||||||||  || |||| ||  ||||||| ||| | ||||| ||||| 
----------------------------------------gtagtttgaagcttgtcgacgttctccgtgttttcagtttcacctcagtttttcgc--agGACGTTGGTCAATATGGATATAAAGCTCGACTTTGTTCCACCTTGGGTGATCAACTTCATCACACGGCAGCTCGTTGGCAGTGGCTACAAACTTTATCAA

upper sequence: LOC_Os11g36070.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ31074 (Selaginella moellendorffii), 3'ss of exon 7
tagtttttaaaatttattcatttgtgattctttttgctcaacaagtttcagtttaataaatatgctgatactccattttttaaccaaatcctccactcagGGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAG
                                          |  ||  || ||    |   |     |  | |   ||| | |  | |  | | |  ||| |  | |  ||||||||||| ||||| ||||| |||||||| ||| | |||||||||||  || |||| ||  ||||||| ||| | ||||| ||||| 
----------------------------------------gtagtttgaagcttgtcgacgttctccgtgtttccagtttcacctcagtgtttcgc--agGACGTTGGTCAATATGGATATAAAGCTCGACTTTGTTCCACCTTGGGTGATCAACTTCATCACACGGCAGCTCGTTGGCAGTGGCTACAAACTTTATCAA

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|58606537|gb|CK034570.1|CK034570
EST:     GTCGGAGGCTTTGTTTTGCAAAGGATTACAAAGGAGAAAAGCTTTTTCAG                         GGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTAT
genomic: GTCGGAGGCTTTGTTTTGCAAAGGATTACAAAGGAGAAAAGCTTTTTCAGgtaaaacatc ... ctccactcagGGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTAT
EST: gi|88273561|gb|CI393967.1|CI393967
EST:     GTCGGAGGCTTTGTTTTGCAAAGGATTACAAAGGAGAAAAGCTTTTTCAG                         GGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTAT
genomic: GTCGGAGGCTTTGTTTTGCAAAGGATTACAAAGGAGAAAAGCTTTTTCAGgtaaaacatc ... ctccactcagGGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTAT
EST: gi|27576960|gb|CA999654.1|CA999654
EST:     GTCGGAGGCTTTGTTTTGCAAAGGATTACAAAGGAGAAAAGCTTTTTCAG                         GGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTAT
genomic: GTCGGAGGCTTTGTTTTGCAAAGGATTACAAAGGAGAAAAGCTTTTTCAGgtaaaacatc ... ctccactcagGGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTAT
EST: gi|27578183|gb|CB000878.1|CB000878
EST:     GTCGGAGGCTTTGTTTTGCAAAGGATTACAAAGGAGAAAAGCTTTTTCAG                         GGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTAT
genomic: GTCGGAGGCTTTGTTTTGCAAAGGATTACAAAGGAGAAAAGCTTTTTCAGgtaaaacatc ... ctccactcagGGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTAT
EST: gi|25778077|gb|CA752829.1|CA752829
EST:     GTCGGAGGCTTTGTTTTGCAAAGGATTACAAAGGAGAAAAGCTTTTTCAG                         GGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTAT
genomic: GTCGGAGGCTTTGTTTTGCAAAGGATTACAAAGGAGAAAAGCTTTTTCAGgtaaaacatc ... ctccactcagGGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcagtttaataaatatgctgatactccattttttaaccaaatcctccactcagGGCAATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAG
                                ttttaac  putative branch site (score: 2)
                                           tcctccactc  putative PPT
      tttaataaatatgct  TA-rich tract