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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctatttatttttttccttaatttttccttttttgttctgattaactatatagaaagaactgcaacacaactagttgcagagcagtattggaatgtt...

Basic information

species Oryza sativa
transcript LOC_Os03g49420.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49420.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G033619_T01 (Zea mays), 5'ss of exon 18
GTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctat------ttatttttttccttaatttttccttttttgttctgattaact---atatagaaagaactgcaacacaactagttgcagagcag-tattggaatgtt-----------------------------------------------------------------------------------------
||| || |||||||||||||||||||| || |||||||||||||||||||| ||| ||||||| ||||||||| |      || || ||||||| ||| ||   || ||| |  |      ||    | |   |||  ||     | |  | | |  |  |||  | ||| |  |||                                                                                         
GTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttagccttttcttattttcctcaatcttgttttctttatattatcccccttctgtttcccaaggtctatggaata--tggataaactgcaactcttgaaccgtttaaaagaccatcatttggaggaaactgagctatccaagtgacaggagcattatttacttaacttgatctgccttttgtatggaatgcag

upper sequence: LOC_Os03g49420.4 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G033619_T02 (Zea mays), 5'ss of exon 17
---------------------------------GTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctat------ttatttttttccttaatttttccttttttgttctgattaact---atatagaaagaactgcaacacaactagttgcagagcag-tattggaatgtt-----------------------------------------------------------------------------------------
                                 ||| || |||||||||||||||||||| || |||||||||||||||||||| ||| ||||||| ||||||||| |      || || ||||||| ||| ||   || ||| |  |      ||    | |   |||  ||     | |  | | |  |  |||  | ||| |  |||                                                                                         
CTATTATTTTTTCGTGTAATCAACGTTCAACAGGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttagccttttcttattttcctcaatcttgttttctttatattatcccccttctgtttcccaaggtctatggaata--tggataaactgcaactcttgaaccgtttaaaagaccatcatttggaggaaactgagctatccaagtgacaggagcattatttacttaacttgatctgccttttgtatggaatgcag
















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|88849788|gb|CI001494.1|CI001494
EST:     TGGGTCATAACAACCAGTATCTTCCCAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCCACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|86597066|gb|CI272661.1|CI272661
EST:     TGGGTCATAACCACCAGTATCTTCCAAAGATTGTCCCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACCAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|29629841|gb|CB634850.1|CB634850
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|27576974|gb|CA999668.1|CA999668
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|29629241|gb|CB634252.1|CB634252
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|29679232|gb|CB675507.1|CB675507
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
EST: gi|29681491|gb|CB677766.1|CB677766
EST:     TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTTTATTTTTGCGGAG                         ATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG
genomic: TGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctattt ... atggatgcagATATTATGTGCGGGTAAGGATCTGGCAACAGAACAAACTTTTAGTAAGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctatttatttttttccttaatttttccttttttgttctgattaactatatagaaagaactgcaacacaactagttgcagagcagtattggaatgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaagaa