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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggatttcatttgtgacattggttttgtgcactttatagtatgaaagaagagacatgactgatgatctttgtaatcattgtttgcatactccattgtagGTTTATGAGCGTATAAAAGCACCACTGCTTACTCTTGTAGGAGCTGGGAGTCCTGAACAATCATATTCTGTGCTATGCCATTTGCATCTTTTGGTGATGC

Basic information

species Oryza sativa
transcript LOC_Os01g43630.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43630.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AC198725.4_FGT007 (Zea mays), 3'ss of exon 6
--atggatttcatttgtgacattggttttgtgcactttatagtatgaaagaagagacatgactgatgatctttgtaatcattgtttgcatactccattgtagGTTTATGAGCGTATAAAAGCACCACTGCTTACTCTTGTAGGAGCTGGGAGTCCTGAACAATCATATTCTGTGCTATGCCATTTGCATCTTTTGGTGATGC
   |  ||| |||     || ||  || | || | ||   |   |    |   |    |      | || |||||  |   | ||||| | |||  || ||||||||||| ||||| ||||||||  |||||||||| || || ||||| ||||||||||| ||||| ||||||||||||||| | |||||| |||||||||
ttcttaattccatggac-actttatttctttggatttctcatgtttctgggttattttttttgtcttatttttgtgttttatttttgc-tcctctgttttagGTTTATGAACGTATTAAAGCACCCTTGCTTACTCTGGTGGGTGCTGGCAGTCCTGAACAGTCATACTCTGTGCTATGCCATCTACATCTTCTGGTGATGC

upper sequence: LOC_Os01g43630.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G029077_T01 (Zea mays), 3'ss of exon 4
-------atggatttcatttgtgacattggttttgtgcactttatagtatgaaagaagagacatgactgatgatctttgtaatcattgtttgcatactccattgtagGTTTATGAGCGTATAAAAGCACCACTGCTTACTCTTGTAGGAGCTGGGAGTCCTGAACAATCATATTCTGTGCTATGCCATTTGCATCTTTTGGTGATGC
       |||| ||  |||| |    ||  |||||||   |||    |||   |  ||     ||   || ||||  | |||||  | || || |  |   || ||||||||||| ||||| ||||||||  |||||||||| || || ||||| ||||||||||| ||||| ||||||||||||||| | |||||| |||||||||
catgtttatgggtt--attttttgtcttatttttgtg---tttgatttatctcatcagcc-tttggtggaagatccatctaatctcttttagc-tcttatgttttagGTTTATGAACGTATTAAAGCACCCTTGCTTACTCTGGTGGGTGCTGGCAGTCCTGAACAGTCATACTCTGTGCTATGCCATCTACATCTTCTGGTGATGC
















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|66915427|gb|CX102275.1|CX102275
EST:     GTTTTTC-CCACTTGACAATGTC-ATGACTGATGTTCACCAGCAG                         GTTTATGAGCGTATAAAAGCACCACTGCTTACTC-TGTAGGAGCTGGGAGT
genomic: GTTTTTCTCCACTTGACAATGTCAATGACTGATGTTCACCAGCAGgtcttactct ... tccattgtagGTTTATGAGCGTATAAAAGCACCACTGCTTACTCTTGTAGGAGCTGGGAGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaagagacatgactgatgatctttgtaatcattgtttgcatactccattgtagGTTTATGAGCGTATAAAAGCACCACTGCTTACTCTTGTAGGAGCTGGGAGTCCTGAACAATCATATTCTGTGCTATGCCATTTGCATCTTTTGGTGATGC
            gactgat  putative branch site (score: 3)
                                            ctccatt  putative PPT
                       tttgtaat  TA-rich tract