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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaacaaacaacagaagcaaacagcttattgccatctcactgaaacttcttcagattcagctaggaacaatagctgaacatccatccatctctgaatctgaatgtctttgacctttcag

Basic information

species Oryza sativa
transcript LOC_Os06g36560.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36560.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G126900_T02 (Zea mays), 5'ss of exon 4
ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaacaaacaacagaagcaaacagcttattgccatctcactgaaacttcttcagattcagctaggaacaatagctgaacatccatccatctctgaatctgaatgtctttgacctttcag
| |||||||||||||||||||| || ||||| ||||||||||| |||||| | |||||||||||| ||     ||     || |       | |   ||   ||| ||| ||| ||   |  | |  | | |  |                                                
ACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGgtaagcaaggggaaatcttggcga----tgcaatataat---actcaaaattcctcctctgaaacctgtagctttcag---------------------------------------------
















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|29644701|gb|CB649708.1|CB649708
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|29679307|gb|CB675582.1|CB675582
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|29660840|gb|CB657115.1|CB657115
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|58587863|gb|CF986171.1|CF986171
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|29661872|gb|CB658147.1|CB658147
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|29656267|gb|CB652542.1|CB652542
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|29676120|gb|CB672395.1|CB672395
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|29656245|gb|CB652520.1|CB652520
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|29680345|gb|CB676620.1|CB676620
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|29657369|gb|CB653644.1|CB653644
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|29642558|gb|CB647565.1|CB647565
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|29669886|gb|CB666161.1|CB666161
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|29639892|gb|CB644901.1|CB644901
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|87031847|gb|CI272548.1|CI272548
EST:     AGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: AGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|66920340|gb|CX107188.1|CX107188
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|29658930|gb|CB655205.1|CB655205
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|87009635|gb|CI309156.1|CI309156
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
EST: gi|29659887|gb|CB656162.1|CB656162
EST:     GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG                         GTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA
genomic: GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaaca ... gacctttcagGTGACACCTTCCCCGTCGGCTGCGCATTCGACGAATGCAACGTCCACTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCGgtaagaaacaaacaacagaagcaaacagcttattgccatctcactgaaacttcttcagattcagctaggaacaatagctgaacatccatccatctctgaatctgaatgtctttgacctttcag

- - - - - - TGCTGC
- - - - - -  GCTGCT
- - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - GGAGCT