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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcacctgcagtttttatgctataacgatcaatattaactattggaggctacttttccttacctgttgttatttttcttcgtgcagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAA

Basic information

species Oryza sativa
transcript LOC_Os03g14980.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G030422_T02 (Zea mays), 3'ss of exon 14
----------------gtgcacctgcagtttttatgctataacgatcaatattaactattggaggctacttttccttacctgttgttatttttcttcgtg--cagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAA
                   |||   |   ||    || ||   | | | | |  || || | |  ||| |  |  |  | | || | ||| || ||| ||  ||||||||||||||||||||||| ||||| ||||| ||||| ||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| |
gtatttgttcagttattatcacagactaattgatagccattttggtgattttgtaccatcgaaaactaatggttttatcttattat-attcttattcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 14
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 13
----------gtgcacctgcagtttttatgctataacgatcaatattaact--attggaggctacttttccttacctgttgttatttttcttcg--tgcagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAA
           |||    |  ||  ||| |  ||     || || |  |||  |||| |    |     ||| |  |  | | | |   || |   | ||||| || |||||||| ||| | ||||| |||||||| |||||||| ||||||    | ||||| ||||||||||| ||||| || || ||||||||||| |
cttatttaagctgccaacgaggtagtta-gaaatgtgcttctatctgtactgcattgtacagcatgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 14
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 13
----------gtgcacctg--cagtttttatgctataacgatc-aatattaactat-tggaggctacttttccttacctgttgttatttttcttcgtgcagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAA
          ||| |      ||    |   |  ||    |||  | ||   |  | ||| |  ||      || |||| | | |    |  |  |  ||||| || |||||||| ||| | ||||| |||||||| || ||||| ||||||  | | || || ||||||||||||||||| ||||| ||||||||||| |
ttagccccatgtgaattaaaacaaaaatggagtaattcgtatctgaaatgtgcggtgtggtgtgtaaaacctctgacctttggatgacctcgtatgc-cagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA

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|29628402|gb|CB633413.1|CB633413
EST:     ATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAAGAAAATATTCAG                         TTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGA
genomic: ATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAGgtgcacctgc ... cttcgtgcagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGA
EST: gi|29671653|gb|CB667928.1|CB667928
EST:     ATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAG                         TTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGAT
genomic: ATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAGgtgcacctgc ... cttcgtgcagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGAT
EST: gi|29625346|gb|CB630357.1|CB630357
EST:     ATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAG                         TTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATG
genomic: ATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAGgtgcacctgc ... cttcgtgcagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATG
EST: gi|58667991|gb|CK056677.1|CK056677
EST:     ATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAG                         TTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGAT
genomic: ATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAGgtgcacctgc ... cttcgtgcagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGAT
EST: gi|29622174|gb|CB627185.1|CB627185
EST:     ATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAG                         TTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGAT
genomic: ATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAGgtgcacctgc ... cttcgtgcagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGAT
EST: gi|29631515|gb|CB636524.1|CB636524
EST:     ATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAG                         TTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGAT
genomic: ATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAGgtgcacctgc ... cttcgtgcagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattaactattggaggctacttttccttacctgttgttatttttcttcgtgcagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAA
                    cttttccttacctgtt  CT-rich tract
                                  ttgttatttttctt  TA-rich tract