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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCTCGCCAAGGCCATCGCCAAGGAGTCAGGCGCCGTCTTCATCAATGTCAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccgcgcgcaaatccttcggtttaactgccgctccttttcatttgtttgttgttatcgctgctgatttatgaaacatcttgcag

Basic information

species Oryza sativa
transcript LOC_Os06g50050.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50050.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G158136_T01 (Zea mays), 5'ss of exon 2
ATGCTCGCCAAGGCCATCGCCAAGGAGTCAGGCGCCGTCTTCATCAATGTCAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagc---tccgcgcgcaaatccttcggtttaact-gccgctcc--ttttcatttgtttgttgttatc--gctgctgatttatgaaacatcttgcag--
|||||||||||||||||||||| |||||| |||||||||||||||||||||||||| ||||| |||||||||||||||||||| ||||| |||||||| ||| |||   ||    |     |  | |   |   || |||| |    |  | ||    | | | |   |  | |   |||| || | |  | | | ||  
ATGCTCGCCAAGGCCATCGCCAGGGAGTCCGGCGCCGTCTTCATCAATGTCAGGATCTCCAATCTCATGAGCAAGTGGTTCGGGGACGCACAGAAGCTTGgtgagcaattctattcttggtttatcctactactcttgccggtttggtgctaatccactggatatccgcctgttttggattcataacaattgtagtagac

upper sequence: LOC_Os06g50050.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G075584_T02 (Zea mays), 5'ss of exon 2
ATGCTCGCCAAGGCCATCGCCAAGGAGTCAGGCGCCGTCTTCATCAATGTCAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagct-ccgcgcgcaaatccttcgg---tttaactg-ccgctccttttcatt---tgtttgttgttatcgctgctgatttatgaaacatcttgcag--
||||||||||||||||| |||| |||||| || ||||||||||||||||||||||| ||||| |||||||||||||||||||| ||||| |||||||||||| |||       | | | |||   ||   |  | ||  || |   |||| | |   |   | ||| |||    |  |  || ||  | ||  | |    
ATGCTCGCCAAGGCCATTGCCAGGGAGTCCGGTGCCGTCTTCATCAATGTCAGGATCTCCAATCTCATGAGCAAGTGGTTCGGGGACGCGCAGAAGCTCGgtgagcaattatactctagtccactggatatccagctatccaccggttttgaatccatacctattgctattatagtagtcttttgccatattcttctttt

upper sequence: LOC_Os06g50050.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S83_145V6.1 (Physcomitrella patens), 5'ss of exon 2
ATGCTCGCCAAGGCCATCGCCAAGGAGTCAGGCGCCGTCTTCATCAATGTCAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccgcgcgcaaatccttcggtttaactgccgctccttttcatttgtttgttgttatcgctgct-gatttatgaaacatcttgcag----------------------------------------------------------------------
 | || || ||||| || |||||||||||| | || || |||||||||||| | || || ||  | |||||||||||||| ||||| || |||||||| |||    ||         ||  ||| | ||   |   |    |||| ||  | ||| |        ||   ||| ||  ||    | || |                                                                       
CTTCTGGCGAAGGCTATTGCCAAGGAGTCACGTGCTGTTTTCATCAATGTCCGCATATCAAATTTGATGAGCAAGTGGTTTGGCGATGCTCAGAAGCTAGgtacaatcttttgaagcatgattccgattg--ttgtgtgagttttgatgggcttgatacagcaaatgtcagatctagtaagtgacatgtaactcatatttagtatttgaagaatcacgaatggagagcccggcagtacttaacgacgaccttgatttgcag

upper sequence: LOC_Os06g50050.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ08867 (Selaginella moellendorffii), 5'ss of exon 2
ATGCTCGCCAAGGCCATCGCCAAGGAGTCAGGCGCCGTCTTCATCAATGTCAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccgcgcgcaaatccttcggtttaactgccgctccttttcatttgtttgttgttatcgctgctgatttatgaaacatcttgcag
 |||| |||||||| || |||||||||||  | |||||||||||||| ||| ||||| |||  ||||||  |||||||||||| ||||| |||||||||||| | |  | | | |   ||||    ||   | || |||      ||   |   |||    | |   ||  ||  || |           
TTGCTGGCCAAGGCGATTGCCAAGGAGTCGCGAGCCGTCTTCATCAACGTCCGGATTGCCACTCTCATGTCCAAGTGGTTCGGAGACGCTCAGAAGCTCGgtaaacctctc-ctcctctcctcgctttcttcggctgcttgccgccaaccgc--gtttcacttgactcttgttggtgcag----------

upper sequence: LOC_Os06g50050.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ11944 (Selaginella moellendorffii), 5'ss of exon 2
ATGCTCGCCAAGGCCATCGCCAAGGAGTCAGGCGCCGTCTTCATCAATGTCAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccgcgcgcaaatccttcggtttaactgccgctccttttcatttgtttgttgttatcgctgctgatttatgaaacatcttgcag
 |||| |||||||| || |||||||||||  | |||||||||||||| ||  ||||| |||  ||||||  |||||||||||| |||||||||||||||||| | |  | | | |     | ||| |||     |  |  | ||||| |||  | |||||   || |                       
TTGCTGGCCAAGGCGATTGCCAAGGAGTCGCGAGCCGTCTTCATCAACGTTCGGATTGCCACTCTCATGTCCAAGTGGTTCGGAGACGCCCAGAAGCTCGgtaaacctctccccct--ctcctcgctttcttgccaaccgcgtttcacttgactcttgttggtgcag-----------------------

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|218492085|gb|FG945532.1|FG945532
EST:     TCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCG                         TGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
genomic: TCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccg ... catcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
EST: gi|218479629|gb|FG945760.1|FG945760
EST:     CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCG                         TGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
genomic: CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccg ... catcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
EST: gi|218505299|gb|FG958827.1|FG958827
EST:     CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCG                         TGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
genomic: CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccg ... catcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
EST: gi|29622367|gb|CB627378.1|CB627378
EST:     CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCG                         TGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
genomic: CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccg ... catcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
EST: gi|33654383|gb|CF276997.1|CF276997
EST:     CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCG                         TGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA
genomic: CAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccg ... catcttgcagTGTCTGCTGTATTTAGTCTCGCACACAAGCTGCAGCCGGCTATTATCTTTA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCTCGCCAAGGCCATCGCCAAGGAGTCAGGCGCCGTCTTCATCAATGTCAGGATTTCCAACCTCATGAGCAAGTGGTTCGGCGACGCCCAGAAGCTCGgtcagctccgcgcgcaaatccttcggtttaactgccgctccttttcatttgtttgttgttatcgctgctgatttatgaaacatcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC