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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGgtataatatgcatatatcatatgtatatgcattgttgttatgatttgtagtcacgtatctctctgtgtttgccatgtattttgggcatctgttattctgtctctcttattatatttcttctttgtggtggtcatatttgctcattgctgttctctttatccaactgtttag

Basic information

species Oryza sativa
transcript LOC_Os02g47220.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47220.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 12
ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGgtataatatgcatatatcatatgtatatgcattgttgttatgatttgt-agtcacgtatctctctgtgtttgccatgtattttgggcatctgttattctgtctctcttattatatttcttctttgtggtggtcatatttgctcattgctgttctctttatccaactgtttag
|||||||||| ||||||||||||||||| |||||||||||||| |||||||| |||||||| || |||||  |||||      |    |||       ||| || ||    |||| | ||||  |||| |   || || |      | |||| || ||   | | || ||    |   | ||||  |                                                    
ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAGgta--atatg-----gttgactgt-------ttgctggtaaagcttgtcactcacaaatcttttgctgctttct-----tgttggtcaccttaaagtttgacttatct--caaatttaatg---------------------------------------------------

upper sequence: LOC_Os02g47220.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 11
ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGgtataatatgcatatatcatatgtatatgcattgttgttatgatttgtagtcacgtatctctctgtgtttgccatgtattttgggcatctgttattctgtctctcttattatatttcttctttgtggtggtcatatttgctcattgctgttctctttatccaactgtttag
|||||||||| ||||||||||||||||| ||| |||||||||| |||||||| |||||||| || |||||  |||||      |    |||  ||||  || |   | | || | | ||||  |||| |   || |     ||| |  ||      |||| |||       |||| ||| |  | |                                                    
ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGgta--atatg-----gttgactgtgcatgc--tgcta--aagcttggcactcacaaatctgt---tgctcaatttgtttgctgctttcttgttgttcaa-----cttaatatttgacct----------------------------------------------------

upper sequence: LOC_Os02g47220.3 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S479_13V6.1 (Physcomitrella patens), 5'ss of exon 7
---------------------------------ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGgtataatatgca-tatatcatatgtatatgcattgttgttatgatttgtagtcacgtatctctctgtgtttgccatgtattttgggcatctgttattctgtctctcttattatatttcttctttgtggtggtcatatttgctcattgctgttctctttatccaactgtttag
                                 || |||||||| |||| || ||||||||||| || || ||||||| ||| |||||||||||  |||||||   |||  | ||||  |  |  |      ||  ||   |||       ||| || |     ||| |  ||    |   || |        ||  |  |                                                                       
TTCTGCAGTCACCAACCTACTCCGCCGCTATAGATGTGTGGGCTGTGGGAGCAATAATGGCCGAACTCTTCACACTTCGTCCACTTTTTCCTGGAGCAAGgtagggtatcaactatactaacttgactaaattttctgcgttgac--acgatcatgtgttaagatgtttcagcagcattcgttagttgatacctaggcaatg----------------------------------------------------------------------

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|58660884|gb|CK049564.1|CK049564
EST:     GCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG                         TGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCG
genomic: GCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGgtataatatg ... aactgtttagTGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCG
EST: gi|58595654|gb|CK006182.1|CK006182
EST:     ACTTCATCCTCTTTTTCCTGGCACAAG                         TGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGA
genomic: ACTTCATCCTCTTTTTCCTGGCACAAGgtataatatg ... aactgtttagTGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGA
EST: gi|163923153|gb|EG709322.1|EG709322
EST:     GCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG                         TGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGA
genomic: GCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGgtataatatg ... aactgtttagTGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGA
EST: gi|88256807|gb|CI354588.1|CI354588
EST:     GCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG                         TGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGTTAGCCCAGATGA
genomic: GCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGgtataatatg ... aactgtttagTGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGA
EST: gi|33797218|gb|CF324473.1|CF324473
EST:     GCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG                         TGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGA
genomic: GCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGgtataatatg ... aactgtttagTGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGA
EST: gi|88664333|gb|CI687436.1|CI687436
EST:     GCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG                         TGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGA
genomic: GCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGgtataatatg ... aactgtttagTGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGA
EST: gi|58675617|gb|CK064304.1|CK064304
EST:     GCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG                         TGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGA
genomic: GCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGgtataatatg ... aactgtttagTGAGGCTGATGAGATTCTGAAGATTTGCAATGTTATCGGTAGCCCAGATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAGgtataatatgcatatatcatatgtatatgcattgttgttatgatttgtagtcacgtatctctctgtgtttgccatgtattttgggcatctgttattctgtctctcttattatatttcttctttgtggtggtcatatttgctcattgctgttctctttatccaactgtttag

- - - - - - - - - - - - - - -  GCTGTT