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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagagtttccttattcctttcaaaatataagacactgtatggtttttaattaaatcttacaattcccttttcttgtccagCACCAAGTGGGATATCGAGTAGAGGATTAAGCAATGGTACATACGAATATAGTAGACGCGTATTTGGTTCTGTTCTGAATGACGTTAGCCGTCGTACTGA

Basic information

species Oryza sativa
transcript LOC_Os05g35274.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g35274.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G175676_T05 (Zea mays), 3'ss of exon 3
gtgagagagtttccttattcctttcaaaatataagacactgtatggtttttaattaaatcttacaattcccttttcttgtccagCAC---CAAGTGGGATATCGAGTAGAGGATTAAGCAATGGTACATACGAATATAGTAGACGCGTATTTGGTTCTGTTCTGAATGACGTTAGCCGTCGTACTGA
|||||  |   ||  |  || |||   |||  |||  | |||    || |   |||| ||| |||| |||| |||  || |||||||   | |||||| || ||| ||||||| ||||||| |||||||| ||||||||||| || ||||||||||||||||||||||| |||||||||||  |   
gtgaggaaaactc--tggtcattttggaatccaagttaatgttgaattatgtgttaagtctcacaactccccttt--tgaccagCACTGTCGAGTGGGTTACCGAATAGAGGACTAAGCAACGGTACATATGAATATAGTAGGCGTGTATTTGGTTCTGTTCTGAATGATGTTAGCCGTCGAGC---

upper sequence: LOC_Os05g35274.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G111596_T02 (Zea mays), 3'ss of exon 2
gtgagagagtttccttattcctttcaaaatataagacactgtatg----gtttttaattaaatcttacaattcccttttcttgtccagCACCAAGTGGGATATCGAGTAGAGGATTAAGCAATGGTACATACGAATATAGTAGACGCGTATTTGGTTCTGTTCTGAATGACGTTAGCCGTCGTACTGA
|||||  |    |  |  || |||   |||  || ||| |  |||     || |   |||| ||| |||| | || |||      || |  |||||||| || ||||||||||| ||||||| |||||||| |||||||||||||| ||||||||||||||||||||||| |||||||||||  |   
gtgaggaaa--actatgatcattttggaatgcaaaacatttaatgttgaattatgtgttaagtctcacaacttcccttttgccagCACCGTCAAGTGGGTTACCGAGTAGAGGACTAAGCAACGGTACATATGAATATAGTAGACGTGTATTTGGTTCTGTTCTGAATGATGTTAGCCGTCGAGC---
















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|313079980|gb|HO213300.1|HO213300
EST:     CAGGATTGCTGGTATTTCTCCAAACCATTCTTATAGTGCGCACTCTGAGG                         CACCAAGTGGGATATCGAGTAGAGGATTAAGCAATGGT
genomic: CAGGATTGCTGGTATTTCTCCAAACCATTCTTATAGTGCGCACTCTGAGGgtgagagagt ... tcttgtccagCACCAAGTGGGATATCGAGTAGAGGATTAAGCAATGGT
EST: gi|66918111|gb|CX104959.1|CX104959
EST:     CAGGATTGCTGGTATTTCTCCAAACCATTCTTATAGTGCGCACTCTGAGG                         CACCAAGTGGGATATCGAGTAGAGGATTAAGCAATGGTACATACGAATATA
genomic: CAGGATTGCTGGTATTTCTCCAAACCATTCTTATAGTGCGCACTCTGAGGgtgagagagt ... tcttgtccagCACCAAGTGGGATATCGAGTAGAGGATTAAGCAATGGTACATACGAATATA
EST: gi|86855040|gb|CI263107.1|CI263107
EST:     GCGCACTCTGAGG                         CACCAAGTGGGATATCGAGTAGAGGATTAAGCAATGGTACATACGAATATA
genomic: GCGCACTCTGAGGgtgagagagt ... tcttgtccagCACCAAGTGGGATATCGAGTAGAGGATTAAGCAATGGTACATACGAATATA
EST: gi|88847592|gb|CI016085.1|CI016085
EST:     TAGTGCGCACTCTGAGG                         CACCAAGTGGGATATCGAGTAGAGGATTAAGCAATGGTACATACGAATATA
genomic: TAGTGCGCACTCTGAGGgtgagagagt ... tcttgtccagCACCAAGTGGGATATCGAGTAGAGGATTAAGCAATGGTACATACGAATATA
EST: gi|86826941|gb|CI268821.1|CI268821
EST:     CAGGATTGCTGGTATTTCTCCCAACCATTCTTATAGTGCGCACTCTGAGG                         CACCAAGTGGGATATCGAGTAGAGGATTAAGCAATGGTACATACGAATATA
genomic: CAGGATTGCTGGTATTTCTCCAAACCATTCTTATAGTGCGCACTCTGAGGgtgagagagt ... tcttgtccagCACCAAGTGGGATATCGAGTAGAGGATTAAGCAATGGTACATACGAATATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataagacactgtatggtttttaattaaatcttacaattcccttttcttgtccagCACCAAGTGGGATATCGAGTAGAGGATTAAGCAATGGTACATACGAATATAGTAGACGCGTATTTGGTTCTGTTCTGAATGACGTTAGCCGTCGTACTGA
                            atcttac  putative branch site (score: 3)
                                     ttcccttttcttgtcc  putative PPT
            tatggtttttaattaa  TA-rich tract