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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatggttcatgtaacctgcccactatctctcttctttgactcctttctgtatttggttatcgatttttcttttttcttttgttctgtcagATTTCACTGCCTCTGGGCAAGCATCATGGCTGGATAAAATTCAGCAAACTGTACAGAATGTTTTACGAACATTCAACTTTTTCAAGACCCCTGTGGATTT

Basic information

species Oryza sativa
transcript LOC_Os01g16970.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16970.3 (Oryza sativa), 3'ss of exon 7
lower sequence: AC213600.3_FGT002 (Zea mays), 3'ss of exon 8
-gtat-atggttcatgtaacctgcccactatctctcttctttgactcctttctgtatttggttatcgatttttcttttttcttttgttctgtcagATTTCACTGCCTCTGGGCAAGCATCATGGCTGGATAAAATTCAGCAAACTGTACAGAATGTTTTACGAACATTCAACTTTTTCAAGACCCCTGTGGATTT
  ||| |   ||||||||   |    | |||  | || ||   |  | | | |   ||  || || ||||| |   | ||  |||| | | |||||||| ||||   | || || ||||| ||| |||| ||| ||||||| |||||||| |||||||| | || |||||||| ||| ||||||||||| |||||
gttatcaccattcatgtagtgt----aatatggcactactactatccttgttttgtttatgtgattgatttattaatattggtttgctatttcagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAGTTCAGCAGACTGTACAAAATGTTTTCCAAAAATTCAACTCTTTTAAGACCCCTGTAGATTT

upper sequence: LOC_Os01g16970.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G052875_T02 (Zea mays), 3'ss of exon 8
gtatatggttcatgtaacctgcccactatctctcttctttgactcctttctgtatttggttatcgatttttcttttttcttttgttctgtcagATTTCACTGCCTCTGGGCAAGCATCATGGCTGGATAAAATTCAGCAAACTGTACAGAATGTTTTACGAACATTCAACTTTTTCAAGACCCCTGTGGATTT
     || |     |   | ||     |  |  || |||    |  | | | ||| || || | ||||| |   | ||  |||| | |  ||||||| ||||   | || || ||||| ||| |||| ||||||||||| ||||||||||||||||| | || |||||||||||| | ||||||||| |||||
----gtgatcaccat--tcagctagtgacatgactacttc--ttgttctgtttatgtgattct-gatttgttaatgtttatttgctattccagATTTAACTGAGCCAGGACATGCATCGTGGTTGGACAAAATTCAGCAGACTGTACAGAATGTTTTCCAAAAATTCAACTTTTTTAGGACCCCTGTAGATTT
















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|58589761|gb|CF988069.1|CF988069
EST:     TGTTGCGTCATACAAGTCTGATGATGATCAGAAAGGTGATGACCATTCAG                         ATTTCACTGCCTCTGGGCAAGCATCATGGCTGGATAAAGTTCAGCAAACTG
genomic: TGTTGCGTCATACAAGTCTGATGATGATCAGAAAGGTGATGACCATTCAGgtatatggtt ... gttctgtcagATTTCACTGCCTCTGGGCAAGCATCATGGCTGGATAAAATTCAGCAAACTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgactcctttctgtatttggttatcgatttttcttttttcttttgttctgtcagATTTCACTGCCTCTGGGCAAGCATCATGGCTGGATAAAATTCAGCAAACTGTACAGAATGTTTTACGAACATTCAACTTTTTCAAGACCCCTGTGGATTT
 ctttgac  putative branch site (score: 4)
                     ttatcgatttttcttt  putative PPT
                           atttttcttttttctt  TA-rich tract