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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaactgcatttttgttcctttatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTTGCAACCTGACAAGGGACTGACATGGCAAATGACAAAACGGCGAGGTGAT

Basic information

species Oryza sativa
transcript LOC_Os02g19510.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G006507_T02 (Zea mays), 3'ss of exon 8
gtaagaactgcatttttgt-------tcctttatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTTGCAACCTGACAAGGGACTGACATGGCAAATGACAAAACGGCGAGGTGAT
||||| ||| ||| ||||        |  | | |||||| |  | ||||||   ||   |  |||    ||  ||   |||| |||||| ||||| |||||| | ||||||||| | || ||||||||||||||||| |||||||| || ||||| |||||||||||||| |||||||| ||||| 
gtaagcactacatatttgcattcttgttttctttctgttcagttggtgttcatttttattaagatgcccttgctat--ttttacagGTACATTGAGCTTGTTCGAAAGCATGGGTTGGAAATCTCTCAGCCTGGTTTACAACCTGATAAAGGACTAACATGGCAAATGACTAAACGGCGTGGTGAC

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G119725_T02 (Zea mays), 3'ss of exon 8
gtaagaactgcatttttgt-------tcctttatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTTGCAACCTGACAAGGGACTGACATGGCAAATGACAAAACGGCGAGGTGAT
||||| ||| ||| |||         |  | | |||||| | |  ||||||   |||  |   ||    ||  ||   |||| |||||| ||||| |||||||| ||||||||| | || |||||||||||||||||||||||||| |  ||||| |||||||||||||| |||||||| ||||| 
gtaagcactacatatttccattcttgttttctttctgttcagcaggtgttcattttgattaaaatgtccttcctat--ttttacagGTACATTGAGCTTGTTAGAAAGCATGGGTTGGAAATCTCTCAGCCTGGTTTGCAACCTGATAGAGGACTAACATGGCAAATGACTAAACGGCGTGGTGAC
















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|38475807|gb|CF959940.1|CF959940
EST:     ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAA                         GTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
genomic: ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactg ... tctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
EST: gi|33795503|gb|CF323621.1|CF323621
EST:     ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAA                         GTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
genomic: ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactg ... tctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
EST: gi|33675555|gb|CF303794.1|CF303794
EST:     ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAA                         GTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
genomic: ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactg ... tctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
EST: gi|86906524|gb|CI294647.1|CI294647
EST:     ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAA                         GTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
genomic: ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactg ... tctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTTGCAACCTGACAAGGGACTGACATGGCAAATGACAAAACGGCGAGGTGAT
    tgttgac  putative branch site (score: 3)
                                      tttgtactctttttc  putative PPT
                                attatgttt  TA-rich tract