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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAATGGGAAGTGAAACTTAAGTTGGACTGCGATGGTCCTGCCAGTGGTACCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGATgtaagtttaatcctctagcattttgttttctttggaaaagcatgtgattttaagccggctggtcctcatacccagacctagtgatctttatatagtgtagacatttttctaactgcttttaattgttttag

Basic information

species Oryza sativa
transcript LOC_Os05g22940.1
intron # 32
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g22940.1 (Oryza sativa), 5'ss of exon 32
lower sequence: AC197672.3_FGT002 (Zea mays), 5'ss of exon 30
CCAATGGGAAGTGAAACTTAAGTTGGACTGCGATGGTCCTGCCAGTGGTACCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGATgtaagtttaatcctctagcattttgttttctttggaaaa-gcatgtgattttaagccggctg--gtcctcatacccagacctagtgatctttatatagtgtagacatttttctaactgc-------ttttaattgttttag
||| ||||| |||||||| ||||||||||| ||||| ||||| ||||||||||||||  | ||||| || ||||| ||||||||||| |||||  | ||||||||||       ||    || | |||| | |  || |  ||||    |||||||    ||  || || |||  | ||  |    |     ||  | |||    || ||   ||   |       || |||| | |||||
CCAGTGGGAGGTGAAACTCAAGTTGGACTGTGATGGACCTGCAAGTGGTACCTGGAGAGTCGTAACTACAAATGTCACTAGTCACACCTGCACCATTGATgtaagttgtccttactgtttttgtattttgtatataacacacatgaagatttaagcaacatgcagttcttatattccgaaatccgaactgccatcca-tgtcattatgttctgaagcacatagtatttctaatggatttag

upper sequence: LOC_Os05g22940.1 (Oryza sativa), 5'ss of exon 32
lower sequence: GRMZM5G858094_T01 (Zea mays), 5'ss of exon 30
CCAATGGGAAGTGAAACTTAAGTTGGACTGCGATGGTCCTGCCAGTGGTACCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGATgtaagtt-----taatcctctagcattttgttttctttggaaaagcatgtgattttaagccggc---tggtcctcatacccagac-ctagtgatctttatatagtgtagacatttttctaactgcttttaattgttttag
||| ||||| |||||||| ||||||||||| ||||| ||||| ||||||||||||||  ||||||| || ||||||||| ||||||| |||||  | ||||||||||     || |  | ||| ||| |||   | ||| | |  |||   | |  ||| |      |||| || |||   |    | |   || |   |||  | |  |       |  | | ||| |||| |||||||
CCAGTGGGAGGTGAAACTCAAGTTGGACTGTGATGGCCCTGCAAGTGGTACCTGGAGAGTTGTAACTACAAATGTTACTGGTCACACCTGCACCATTGATgtaagttgtccctactgttttagtattctgta--cattgcaca--catcacaatacaagtcaatgtgtggttcttatatttaactgccatccatgtcattattttctgaag----cacatagtacttctaatggttttag
















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|58659246|gb|CK047926.1|CK047926
EST:     CCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGAT                         ATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
genomic: CCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGATgtaagtttaa ... attgttttagATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
EST: gi|58672807|gb|CK061493.1|CK061493
EST:     CCTGGAGGATTGTAACAACCAATGTTACGAGTCACACTTGCACTGTGGAT                         ATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
genomic: CCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGATgtaagtttaa ... attgttttagATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
EST: gi|29684015|gb|CB680290.1|CB680290
EST:     GTAACAACCAATGTTCCTAGTCACACTTGCACTGTGGAT                         ATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
genomic: GTAACAACCAATGTTACTAGTCACACTTGCACTGTGGATgtaagtttaa ... attgttttagATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
EST: gi|29681304|gb|CB677579.1|CB677579
EST:     CCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGAT                         ATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
genomic: CCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGATgtaagtttaa ... attgttttagATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
EST: gi|29624333|gb|CB629344.1|CB629344
EST:     CCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGAT                         ATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
genomic: CCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGATgtaagtttaa ... attgttttagATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
EST: gi|33678996|gb|CF307235.1|CF307235
EST:     CCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGAT                         ATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
genomic: CCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGATgtaagtttaa ... attgttttagATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
EST: gi|58691648|gb|CK080335.1|CK080335
EST:     CCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGAT                         ATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
genomic: CCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGATgtaagtttaa ... attgttttagATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
EST: gi|58665399|gb|CK054085.1|CK054085
EST:     CCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGAT                         ATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC
genomic: CCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGATgtaagtttaa ... attgttttagATCTACCGTGAGATGGAAGATAAAGAATCACGGAAGTTAGTATACCATCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAATGGGAAGTGAAACTTAAGTTGGACTGCGATGGTCCTGCCAGTGGTACCTGGAGGATTGTAACAACCAATGTTACTAGTCACACTTGCACTGTGGATgtaagtttaatcctctagcattttgttttctttggaaaagcatgtgattttaagccggctggtcctcatacccagacctagtgatctttatatagtgtagacatttttctaactgcttttaattgttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT