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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgtgctgctaaagctgttactcctttgtttatgtttattgtgcttcaaattgcactatcatctgttttaacaatattgagggatccctttcttttagGTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTGGCTGGTGCAACTCCAGTGATCCTTCCTACAAGCATATCAGAGAATTTCT

Basic information

species Oryza sativa
transcript LOC_Os01g65090.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G400604_T01 (Zea mays), 3'ss of exon 4
gtttgtgctgctaaagctgt-tactcctttgtttat-gtttattgtgcttcaa-att--gcactatcatctgttttaacaatattgagggatccctttcttttagGTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTGGCTGGTGCAACTCCAGTGATCCTTCCTACAAGCATATCAGAGAATTTCT
      | |  |   |   | | |||   || |||| | || | |   |  || |||  |  ||    | |   |||||||| |  |||||||||||| ||| |||||||||| ||||| ||||| ||||||||||||||||||||||||| | |||||| ||| ||||||||||| |||||||||| |||||||||||||||||
-----agatattggtggcatgtcctcagatgattattgcttgtagcattagaatattcggtgctgatgtttagcttaacaatgtcaagggatccctttgtttcagGTTTTGATTCCAGCCCCATATTGGGTCAGTTATCCTGAGATGGCTAGACTGGCTGATGCGACTCCAGTGATTCTTCCTACAAACATATCAGAGAATTTCT
















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|88396984|gb|CI578133.1|CI578133
EST:     AGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGATGAG                         GTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTG
genomic: AGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGATGAGgtttggcctc ... tttcttttagGTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTG
EST: gi|29645872|gb|CB650879.1|CB650879
EST:     AGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGATGAG                         GTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTG
genomic: AGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGATGAGgtttggcctc ... tttcttttagGTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTG
EST: gi|109974688|gb|DT807048.1|DT807048
EST:     TGCCGTTTGCTCACCTGGTGATGAG                         GTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTG
genomic: TGCCGTTTGCTCACCTGGTGATGAGgtttggcctc ... tttcttttagGTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcaaattgcactatcatctgttttaacaatattgagggatccctttcttttagGTTTTGATACCAGCACCATACTGGGTCAGTTATCCTGAGATGGCTACATTGGCTGGTGCAACTCCAGTGATCCTTCCTACAAGCATATCAGAGAATTTCT
                      ttttaac  putative branch site (score: 2)
                                         tccctttctttt  putative PPT
                    tgttttaacaatatt  TA-rich tract