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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtatggcttcgtctagttagttgaacgatatattccatgctactataacatatttcaatatatttcagCTTGTGCTTCGCTTTGCAAACCGTTTGTTCCTACCTCTTTGGAATCGTGATAACATTGCTAATGTACAG

Basic information

species Oryza sativa
transcript LOC_Os02g38840.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g38840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 6
gtaagttgtatg-gcttcgtctagttagttgaacgatatattccatgctactataacatatttcaatatattt-cagCTTGTGCTTCGCTTTGCAAACCGTTTGTTCCTACCTCTTTGGAATCGTGATAACATTGCTAATGTACAG
||||  ||| || ||       |  |   |   |  |||||   |||| ||| |  | |||      || ||| |||||||||||||| ||||||||||| || ||  | ||||| ||||| ||||||||||| ||||| ||||||
gtaatatgtgtgagccatagtgaactgtatatgctttatat---atgcaactgtttcttatactgccatgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAG

upper sequence: LOC_Os02g38840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 6
---gtaagttgt-----atggcttcgtctagttagttgaacgatatattccatgctactataacatatttcaat-atatt-tcagCTTGTGCTTCGCTTTGCAAACCGTTTGTTCCTACCTCTTTGGAATCGTGATAACATTGCTAATGTACAG
   |||| |  |     || |  || ||   ||  |||    ||| | |       |         |||| | |  ||||  ||| | || ||||| ||||||||||| || ||| | ||||| ||||| ||||| |||||||||||||| |||
gtagtaaatgattgcttattggctc-tcatattgcttgcttcataaacttggcctaatccctctccatttgacttgtattaccagTTAGTACTTCGTTTTGCAAACCGATTATTCATGCCTCTATGGAACCGTGACAACATTGCTAATGTGCAG
















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|29616736|gb|CB621748.1|CB621748
EST:     AGCTGTACAGAATTGACCACTATTTAGGAAAAGAATTGGTCCAAAATCTG                         CTTGTGCTTCGCTTTGCAAACCGTTTGTTCCTACCTCTCTGGAATCGTGAT
genomic: AGCTGTACAGAATTGACCACTATTTAGGAAAAGAATTGGTCCAAAATCTGgtaagttgta ... tatatttcagCTTGTGCTTCGCTTTGCAAACCGTTTGTTCCTACCTCTTTGGAATCGTGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttagttgaacgatatattccatgctactataacatatttcaatatatttcagCTTGTGCTTCGCTTTGCAAACCGTTTGTTCCTACCTCTTTGGAATCGTGATAACATTGCTAATGTACAG
                             ctataac  putative branch site (score: 3)
                           tactataacatatttc  TA-rich tract