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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggtatttcttaacttattttgttatataactttgatgatgttagagtcataacttcagatcattctgtaatttaaaatgtccacagTTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAGTTGAGGGAAATGTTCCAAAATCCAGAATTTATTCGCCAGCTTACATCCC

Basic information

species Oryza sativa
transcript LOC_Os10g39620.5
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g39620.6 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G136769_T01 (Zea mays), 3'ss of exon 3
---gtacggtatttcttaacttattttgttatataactttgatgatgttagagtcataacttcagatcattctgtaatttaaaat-gtccacagTTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAGTTGAGGGAAATGTTCCAAAATCCAGAATTTATTCGCCAGCTTACATCCC
   || |    | |   |||||||| | ||   |   |||   ||||||  | |  | || |  |||| || |||  | |    | | ||||||||||||| ||||||||||||| |||||||||| |||||||||||| ||||| |||||||||| || ||||||||||||||| |||||||||| ||||| |
gtagttcaacttgtgccaacttattct-ttgcgttcttttttggatgttgcaattctgacattggatcgttttgtgttctctccttggccacagTTGCTTAGCTTCAACCCAAATGCACGCAACCTGATGGAATCAAACCCTCAGATGAGGGAAATATTTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGC

upper sequence: LOC_Os10g39620.6 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G170843_T02 (Zea mays), 3'ss of exon 3
---gtacggtatttcttaacttattttgttatataactttgatgatgttagagtcataacttcagatcattctgtaatttaaaatgtccacagTTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAGTTGAGGGAAATGTTCCAAAATCCAGAATTTATTCGCCAGCTTACATCCC
   || |    | |   ||||| || |||  | |   |||  | |||||  | |  | || |  |||  || |||   |     || | ||||||||||||| ||||||||||| |||||||||| |||||||||||||||||  ||||||||||||| ||||||||||||||| |||||||||| ||||| |
gtagttcaacttatgccaactttttctgtgctct--tttttgt-atgttgcaattctgacattggattgttttgtt-ctcgccttggctacagTTGCTTAACCTCAACCCAAATGCACGCAACCTGATGGAATCAAACACTCATATGAGGGAAATGTTTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGC
















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|58665177|gb|CK053863.1|CK053863
EST:     TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAG                         TTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
genomic: TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgtacggtatt ... atgtccacagTTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
EST: gi|33812321|gb|CF332050.1|CF332050
EST:     TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAG                         TTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
genomic: TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgtacggtatt ... atgtccacagTTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
EST: gi|58676841|gb|CK065528.1|CK065528
EST:     TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAG                         TTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
genomic: TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgtacggtatt ... atgtccacagTTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
EST: gi|58597929|gb|CK008457.1|CK008457
EST:     TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAG                         TTGCTTAACTTCA
genomic: TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgtacggtatt ... atgtccacagTTGCTTAACTTCA
EST: gi|58681884|gb|CK070571.1|CK070571
EST:     TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAG                         TTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG
genomic: TGATGCAGATGATGCAGAATATCATGTCTGATCCACAGTCCATGAACCAGgtacggtatt ... atgtccacagTTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatgatgttagagtcataacttcagatcattctgtaatttaaaatgtccacagTTGCTTAACTTCAACCCAAATACACGCAACCTCATGGAATCAAACACTCAGTTGAGGGAAATGTTCCAAAATCCAGAATTTATTCGCCAGCTTACATCCC
               tcataac  putative branch site (score: 2)
                              attctgtaatttaaaa  TA-rich tract