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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattcattcattcctctcccgaaatccccccctcctccctccctccctcctcaacaacacatccggatttggattggtttcttctcgatttcttcctttgacagattgcgtgtatattgctaacagtggcaatttcttcgggttcagCAATGCCCAACGTTAGGTCCTCCCCTGTCGCAGATCTTCCTGGATGGCCATTGTTTTCGCCTCCTAAGCTTCAGTTGCAAAAGTGTACCAAGTGTCCCAG

Basic information

species Oryza sativa
transcript LOC_Os09g39660.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g39660.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G142502_T02 (Zea mays), 3'ss of exon 2
gtatattcattcattcctctcccgaaatccccccctcctccctccctccctcctcaacaacaca-tccggatttggattggtttcttctcgatttcttcctttgacagattgcgtgtatattgctaacagtggcaatttcttcgggttcagCAATGCCCAACGTTAGGTCC---TCCCCTGTCG-----CAGATCTTCCTGGATGGCCATTGTTTTCGCCTCCTAAGCTTCAGTTGCAAAAGTGTACCAAGTGTCCCAG---------------------------------
                                              |  ||  |||  ||     |     |||   |||   |  | | |        ||     || |   || |  || |    |||  | |||| |       ||||||||    | |  || |      | |||| | |     |||||||||| || ||||| ||||| |||||||||||| | |||||| | ||||||||||||||  ||||                                 
-------------------------------------------gtatgtcttttcagaaatctggtattcgtttcagttgtgatgatataggcaggcagctccagtaggtgttgt-tggatag---gcagaagaaattcccct--tctcagcaatctaaacctgtatgcttcttttcccttttgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGTGTACCAAGTGCTCCAGAGAATTCTGTTCTGCAATCAACTTCCGGAGGCA

upper sequence: LOC_Os09g39660.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G142502_T03 (Zea mays), 3'ss of exon 2
gtatattcattcattcctctcccgaaatccccccctcctccctccctccctcctcaacaacacatccggatttggattggtttcttctcgatttcttcctttgacagattgcgtgtatattgctaacagtggcaatttcttcgggttcagCAATGCCCAACGTTAGGTCC---TCCCCTGTCG-----CAGATCTTCCTGGATGGCCATTGTTTTCGCCTCCTAAGCTTCAGTTGCAAAAGTGTACCAAGTGTCCCAG---------------------------------
                           |    ||        |   ||  | |  || | |   |     |||   |||   |  | | |        ||     || |   || |  || |    |||  | |||| |       ||||||||    | |  || |      | |||| | |     |||||||||| || ||||| ||||| |||||||||||| | |||||| | ||||||||||||||  ||||                                 
--------------------------gtgagaccgagaaatgtatgtcttttcagaa-atctggtattcgtttcagttgtgatgatataggcaggcagctccagtaggtgttgt-tggatag---gcagaagaaattcccct--tctcagcaatctaaacctgtatgcttcttttcccttttgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGTGTACCAAGTGCTCCAGAGAATTCTGTTCTGCAATCAACTTCCGGAGGCA
















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|117231993|gb|CT853910.1|CT853910
EST:     TCTCATCTTCGGTTCCAATCCAATCCAAG                         CAATGCCCAACGTTAGGTCCTCCCCTGTCGCAGATCTTCCTGGATGGCCAT
genomic: TCTCATCTTCGGTTCCAATCCAATCCAAGgtatattcat ... tcgggttcagCAATGCCCAACGTTAGGTCCTCCCCTGTCGCAGATCTTCCTGGATGGCCAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctttgacagattgcgtgtatattgctaacagtggcaatttcttcgggttcagCAATGCCCAACGTTAGGTCCTCCCCTGTCGCAGATCTTCCTGGATGGCCATTGTTTTCGCCTCCTAAGCTTCAGTTGCAAAAGTGTACCAAGTGTCCCAG
                         tgctaac  putative branch site (score: 1)
                                        tttcttc  putative PPT
                  tgtatatt  TA-rich tract