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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctttaattttaggtagctattgtagatgttcatgttctgttatgcaagtttgagttgctcattggatttgagttgctcattggatttgttcttccagGATCCTTATTTCAGGATGACCCGGGACGTTGCTCCAAGAATTGGTTACCAGAAACCATCATTAATTGAATCGAGATTTTTCCCTGCTCTTCAG

Basic information

species Oryza sativa
transcript LOC_Os12g35570.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 5
---tttctttaattttaggtagctattgtagatgttcatgttctgttatgcaagtttgagttgctcattggatttgagttgctcattggatttgttcttccagGATCCTTATTTCAGGATGACCCGGGACGTTGCTCCAAGAATTGGTTACCAGAAACCATCATTAATTGAATCGAGATTTTTCCCTGCTCTTCAG
   |||   |  || |  | || | |     ||    ||    | | || ||  |||| || |    |   ||||     |   |||    || |||| | ||||||| ||||| |||||||| || || |||||||| ||||||||||| |||||||||||| | |||||||| |||||||| ||||||||||||
atgtttgcctttttctttgaagtt-tgaccaataccaatacattttgatacatctttgtgt-gtctttcaaattttgagagtagatttttcttcttctgc-agGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG

upper sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 6
--tttctttaat-tttaggtagctattgtagatgttcatgt-tctgttatgcaagtttgagttgctcattggatttgagtt-gctcattggatttgttcttccagGATCCTTATTTCAGGATGACCCGGGACGTTGCTCCAAGAATTGGTTACCAGAAACCATCATTAATTGAATCGAGATTTTTCCCTGCTCTTCAG
  | |  | |   ||||   | || ||  |    ||  ||  |||| | |  | ||   | ||  |   |||  |||  || | |   |  ||||||||    |||||||||||||||| ||||| ||||| ||||||||  | || || || || || ||  |||| ||||||||   ||| |||||||| ||||||
aatattgtcatcatttatccaact-ttacattcatttttgcatctgatgtcaatgtaataattattttatggtattgcctttgtttccttaatttgttc----agGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCACAAGCCCGCATTGATTGAATCATTATTCTTCCCTGCCCTTCAG
















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|27576171|gb|CA998865.1|CA998865
EST:     TCTCTGGGAATGACCAACTACGGTGCTTAATCCCATGTGCAATAGACCAG                         GATCCTTATTTCAGGATGACCCGGGACGTTGCTCCAAGAATTGGTTACCAG
genomic: TCTCTGGGAATGACCAACTACGGTGCTTAATCCCATGTGCAATAGACCAGgtataaacat ... gttcttccagGATCCTTATTTCAGGATGACCCGGGACGTTGCTCCAAGAATTGGTTACCAG
EST: gi|117242702|gb|CT843523.1|CT843523
EST:     TCTCTGGGAATGACCAACTACGGTGCTTAATCCCATGTGCAATAGACCAG                         GATCCTTATTTCAGGATGACCCGGGACGTTGCTCCAAGAATTGGTTACCAG
genomic: TCTCTGGGAATGACCAACTACGGTGCTTAATCCCATGTGCAATAGACCAGgtataaacat ... gttcttccagGATCCTTATTTCAGGATGACCCGGGACGTTGCTCCAAGAATTGGTTACCAG
EST: gi|29674926|gb|CB671201.1|CB671201
EST:     TCCCATGTGCAATAGACCAG                         GATCCTTATTTCAGGATGACCCGGGACGTTGCTCCAAGAATTGGTTACCAG
genomic: TCCCATGTGCAATAGACCAGgtataaacat ... gttcttccagGATCCTTATTTCAGGATGACCCGGGACGTTGCTCCAAGAATTGGTTACCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaagtttgagttgctcattggatttgagttgctcattggatttgttcttccagGATCCTTATTTCAGGATGACCCGGGACGTTGCTCCAAGAATTGGTTACCAGAAACCATCATTAATTGAATCGAGATTTTTCCCTGCTCTTCAG
                                          tttgttcttcc  CT-rich tract
                                         atttgtt  TA-rich tract