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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGCAAGAAGGAATGGTTTGGATATGGCCTGGCAATGACCCACCGAAGTCGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggagatcatgtcatgctgcagcaaccatactatgtggaactgtcctgtgcatttcaagatttttactggactgaaaagtaatggaattgttcttgatcatcaacag

Basic information

species Oryza sativa
transcript LOC_Os10g41780.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G082527_T01 (Zea mays), 5'ss of exon 1
TGAGCAAGAAGGAATGGTTTGGATATGGCCTGGCAATGACCCACCGAAGTCGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggagatcatgtcatgctgcagcaaccatactatgtggaactgt-cctgtgcatttcaagatttttactggactgaaaagtaatggaattgttcttgatcatcaacag
|||||| ||||||||||| ||||| |||||| |  |||||||||| ||| | || ||||||||||| ||||||||||||||||||||| |||| ||||||||||||||| ||| ||  ||| |||||   |   | | | | | | |||   | |   |  |    | ||     ||      |  |                          
TGAGCAGGAAGGAATGGTCTGGATTTGGCCTAGGGATGACCCACCAAAGGCTACAATCCCTTCTCTTCTGCCTCCTTCAGGATTTACAGTTCATGCAGAGgtaaaaggaaatcctgctatgatgcagtggcacaagtgtattgtattgtatttttttgtaacggtgtgttcttctgatcatccaacag-------------------------

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G171390_T05 (Zea mays), 5'ss of exon 6
TGAGCAAGAAGGAATGGTTTGGATATGGCCTGGCAATGACCCACCGAAGTCGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggagatcatgtcatgctgcagcaaccatactatgtggaactgtcctgtgcatttcaagatttttactggactgaaaagtaatggaattgttcttgatcatcaacag
|||||| ||||| ||||| ||||| ||||| ||  | |||||||| ||| | || ||||||||||||||||||||||||||||||||  | |||||||||||||||  | |         |||   | |  | ||| |||     |  | |  |||| |  ||  |  | |    || |      | ||    |  |||  ||| |   |||
TGAGCAGGAAGGGATGGTCTGGATCTGGCCCGGGGACGACCCACCCAAGGCTACCATCCCTTCTCTGCTGCCTCCTTCAGGATTTACGGTCCACGCAGAGgtaaaattaaa---------gcta-ggaattcctacaatgcaatgcaatgcaatgcaatgaaatctcctgatgtaacggccggccagtg----ttctctctatctt--gcag

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G171390_T03 (Zea mays), 5'ss of exon 5
TGAGCAAGAAGGAATGGTTTGGATATGGCCTGGCAATGACCCACCGAAGTCGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggagatcatgtcatgctgcagcaaccatactatgtggaactgtcctgtgcatttcaagatttttactggactgaaaagtaatggaattgttcttgatcatcaacag
                                                                 ||||||||||||||||||||||  | |||||||||||||||  | | |  |  || |     | || || | |||     |  | |  || | |       | | ||  | | |   ||                            
-----------------------------------------------------------------TGCTGCCTCCTTCAGGATTTACGGTCCACGCAGAGgtaaaattaaagctaggaattc-----ctacaatgcaatgcaatgcaatgcaatgaaatctcctgatgtaac--ggccggccag----------------------------

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G171390_T04 (Zea mays), 5'ss of exon 5
TGAGCAAGAAGGAATGGTTTGGATATGGCCTGGCAATGACCCACCGAAGTCGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggagatcatgtcatgctgcagcaaccatactatgtggaactgtcctgtgcatttcaagatttttactggactgaaaagtaatggaattgttcttgatcatcaacag
                                                                 ||||||||||||||||||||||  | |||||||||||||||  | |         |||   | |  | ||| |||     |  | |  |||| |  ||  |  | |    || |      | ||    |  |||  ||| |   |||
-----------------------------------------------------------------TGCTGCCTCCTTCAGGATTTACGGTCCACGCAGAGgtaaaattaaa---------gcta-ggaattcctacaatgcaatgcaatgcaatgcaatgaaatctcctgatgtaacggccggccagtg----ttctctctatctt--gcag

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G171390_T01 (Zea mays), 5'ss of exon 5
TGAGCAAGAAGGAATGGTTTGGATATGGCCTGGCAATGACCCACCGAAGTCGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggagatcatgtcatgctgcagcaaccatactatgtggaactgtcctgtgcatttcaagatttttactggactgaaaagtaatggaattgttcttgatcatcaacag
|||||| ||||| ||||| ||||| ||||| ||  | |||||||| ||| | || ||||||||||||||||||||||||||||||||  | |||||||||||||||  | | |  |  || |     | || || | |||     |  | |  || | |       | | ||  | | |   ||                            
TGAGCAGGAAGGGATGGTCTGGATCTGGCCCGGGGACGACCCACCCAAGGCTACCATCCCTTCTCTGCTGCCTCCTTCAGGATTTACGGTCCACGCAGAGgtaaaattaaagctaggaattc-----ctacaatgcaatgcaatgcaatgcaatgaaatctcctgatgtaac--ggccggccag----------------------------

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G038487_T01 (Zea mays), 5'ss of exon 6
TGAGCAAGAAGGAATGGTTTGGATATGGCCTGGCAATGACCCACCGAAGTCGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggagatcatgtcatgctgcagcaaccatactatgtggaactgtcctgtgcatttcaagatttttactggactgaaaagtaatggaattgttcttgatcatc-aacag
|||||| ||||||||||| ||||| ||||||||  |||||||||| ||| | || ||||||||||| ||||||||||||||||||||| | |||||||||||||||||| ||| ||  ||| |||||   | |          || |||  ||||           || || || | || |  |||| ||  | ||||| ||||||| |||||
TGAGCAGGAAGGAATGGTCTGGATTTGGCCTGGGGATGACCCACCAAAGGCTACAATCCCTTCTCTTCTGCCTCCTTCAGGATTTACAGTACACGCAGAGgtaaaaggaaatcctgctatgatgcagtggcaa----------aagtgtattgtg-----------ttgtattgtattgtattgtaacggtgt-gttct-gatcatccaacag

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G136904_T01 (Zea mays), 5'ss of exon 1
TGAGCAAGAAGGAATGGTTTGGATATGGCCTGGCAATGACCCACCGAAGTCGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggagatcatgtcatgctgcagcaaccatactatgtggaactgtcctgtgcatttcaagatttttactggactgaaaagt-aatggaattgttcttgatcatcaacag
|||||| ||||||||||| ||||| ||||||||  |||||||||| ||| | || ||||||||||| ||||||||||||||||||||| |||| ||||||||||||||| ||| ||  ||| |||||   |   | | | | | | |||  | |   | | |   | | | ||   ||||  |   ||  |                      
TGAGCAGGAAGGAATGGTCTGGATTTGGCCTGGGGATGACCCACCAAAGGCTACAATCCCTTCTCTTCTGCCTCCTTCAGGATTTACAGTTCATGCAGAGgtaaaaggaaatcctgctatgatgcagtggcacaagtttattgtattgtattttttttgtaacagtgtgttct--tctgatcatccaacag----------------------

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|29673392|gb|CB669667.1|CB669667
EST:     CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAG                         ATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
genomic: CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggag ... tcatcaacagATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
EST: gi|29618942|gb|CB623954.1|CB623954
EST:     CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAG                         ATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
genomic: CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggag ... tcatcaacagATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
EST: gi|58604859|gb|CK032892.1|CK032892
EST:     CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAG                         ATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
genomic: CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggag ... tcatcaacagATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
EST: gi|38472639|gb|CF956771.1|CF956771
EST:     CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAG                         ATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
genomic: CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggag ... tcatcaacagATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
EST: gi|24208889|gb|AU225916.1|AU225916
EST:     CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAG                         ATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
genomic: CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggag ... tcatcaacagATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
EST: gi|29617556|gb|CB622568.1|CB622568
EST:     CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAG                         ATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
genomic: CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggag ... tcatcaacagATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
EST: gi|29671152|gb|CB667427.1|CB667427
EST:     CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAG                         ATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
genomic: CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggag ... tcatcaacagATAGTGATGGAGCTACCAGTGGAGCATGGACTTCTTCTGGACAATCTATTA
EST: gi|58611249|gb|CK038961.1|CK038961
EST:     CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAG                         ATAGTGATGGAG
genomic: CGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggag ... tcatcaacagATAGTGATGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGCAAGAAGGAATGGTTTGGATATGGCCTGGCAATGACCCACCGAAGTCGACTATCCCTTCTCTGCTGCCTCCTTCAGGATTTACAATTCACGCAGAGgtaaaaggagatcatgtcatgctgcagcaaccatactatgtggaactgtcctgtgcatttcaagatttttactggactgaaaagtaatggaattgttcttgatcatcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC