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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGAACGGGAACTCAAAAGGCAGAGAAGAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgtttgtgcatttcaagctatactggatagaattatcttttgtagtgccttcaattgatgaagcctaacttaaattctgcag

Basic information

species Oryza sativa
transcript LOC_Os12g13170.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g13170.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G074373_T02 (Zea mays), 5'ss of exon 12
GATGAACGGGAACTCAAAAGGCAGAGAAGAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgtttgtgcatttcaagctatactggatagaattatcttttgtagtgccttcaattgatgaagcctaact-taaattctgcag
|||||||| |||||||||||||| | ||||||||| || || ||||||||||| |||||||||||||||||||| |||||| ||||| || ||  |  | || |||||| ||  | ||| || |      |    | |||||| ||   || | | | || |||||
GATGAACGTGAACTCAAAAGGCAAAAAAGAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgttagttcaacttga-ctgtactgggtaccactatgttgt------cagctagttgatggaggacaaatgtgagttttgcag

upper sequence: LOC_Os12g13170.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G088140_T03 (Zea mays), 5'ss of exon 11
GATGAACGGGAACTCAAAAGGCAGAGAAGAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgtttgtgcatttcaagctatactggatagaattatcttttgtagtgccttcaattgatgaagcctaacttaaattctgcag
|||||||  |||||||||| ||| |||||||| || ||||| ||||||||||| || ||||||||||| ||||| |||||| |||||||| ||  |  | || |||||| ||  | ||| ||   ||||         |||||| |   ||  | | || |||||
GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAGgtaattgtttgttcaacttga-ctgtactgggtactactatgttaactagt---------tgatgatgaacaa--tgagttttgcag

upper sequence: LOC_Os12g13170.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA09G34170.1 (Glycine max), 5'ss of exon 12
GATGAACGGGAACTCAAAAGGCAGAGAAGAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgtttgtgcatttcaagctatactg----gatagaattatcttttgtagtgccttcaattgatg-aagcctaacttaaattctgcag
|||||| | || || |||||||| ||  | || || || |||||||| ||||||||||| || |||||||| ||||||||| | |   ||   | |   | | | ||     | | |  | ||| |  ||      |  || |  ||  ||  |  ||||||        
GATGAAAGAGAGCTTAAAAGGCAAAGGCGGAAGCAGTCTAACAGGGAATCTGCTCGCAGGTCCAGGTTGCGCAAGCAGgtaatggagagtcattatagtggtttccttctgtggttggttgatcataagtcacatatctaacttctgtgagtttttcttaaag-------

upper sequence: LOC_Os12g13170.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT2G35530.1 (Arabidopsis thaliana), 5'ss of exon 11
GATGAACGGGAACTCAAAAGGCAGAGAAGAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgtttgtgcatttcaagctatactggatagaattatcttttgtagtgccttcaattgatgaagcctaacttaaattctgcag
|| ||  | ||||| ||  | |||||| | || || ||||| |||||||||||||| ||||| ||||||||||| |||||| |      | ||||| |    |        |     || |   | |     || |   | ||     | | |||          
GACGATAGAGAACTTAAGCGACAGAGACGGAAGCAGTCCAATAGGGAGTCTGCTCGAAGATCAAGGTTGCGTAAACAGgtactaaac-atccattt-agatcacctctagcacgcccatgtga-gcaaattattgacccggtgtt-tgtgatttag---------

upper sequence: LOC_Os12g13170.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G32150.1 (Arabidopsis thaliana), 5'ss of exon 11
GATGAACGGGAACTCAAAAGGCAGAGAAGAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatt-tgtttgtgcat-ttcaagctatactggatagaattatcttttgtagtgccttcaattgat--gaagcctaacttaaattctgcag-------
|||||  | ||  | ||  | |||||| | || |||||||| ||||| |||||||| ||||| ||||||||||| ||||||   |     ||  | ||||||||   ||    || || ||| |   ||     |   | ||||   |||| |  | |    ||| | |       
GATGAGAGAGAGATTAAGCGACAGAGACGGAAGCAATCCAATAGGGAATCTGCTCGTAGATCCAGGTTGCGTAAACAGgtaacataaacatgtttcttcaagctgatct----agcatcatcatgcctatcaagtatgaatgatcaaaagcttttccttttctcttctgtgttcag

upper sequence: LOC_Os12g13170.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv02s0012g02250.t01 (Vitis vinifera), 5'ss of exon 11
GATGAACGGGAACTCAAAAGGCAGAGAAGAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgtttgtgcatttcaagctat-actggatagaattatcttttgtagtgccttcaattgatgaagcctaacttaaattctgcag
|||||| | || || ||||| ||||||||||| || || ||| |||||||||||||| |||| ||||||||||||||||||  |     |    || |  || |   |||      ||    ||| | | |  || |  || |   |  | | | |          
GATGAAAGAGAGCTTAAAAGACAGAGAAGAAAGCAGTCGAACCGGGAGTCTGCTCGCCGATCCAGGTTGCGTAAGCAGgtaacttcagattttgttaatcctgttgatggccttgcttggaatttattgagtgtttatatgtttttg--tgagtcag---------

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|29629931|gb|CB634940.1|CB634940
EST:     GAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGAAGTTTTAAAGCAAGAAAAT
genomic: GAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgttt ... aattctgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGAAGTTTTAAAGCAAGAAAAT
EST: gi|29626016|gb|CB631027.1|CB631027
EST:     GAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGAAGTTTTAAAGCAAGAAAAT
genomic: GAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgttt ... aattctgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGAAGTTTTAAAGCAAGAAAAT
EST: gi|29659468|gb|CB655743.1|CB655743
EST:     GAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGAAGTTTTAAAGCAAGAAAAT
genomic: GAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgttt ... aattctgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGAAGTTTTAAAGCAAGAAAAT
EST: gi|25804027|gb|CA759988.1|CA759988
EST:     GGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGAAGTTTTAAAGCAAGAAAAT
genomic: GGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgttt ... aattctgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGAAGTTTTAAAGCAAGAAAAT
EST: gi|29676440|gb|CB672715.1|CB672715
EST:     GAAACCAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGAAGTTTTAAAGCAAGAAAAT
genomic: GAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgttt ... aattctgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGAAGTTTTAAAGCAAGAAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGAACGGGAACTCAAAAGGCAGAGAAGAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAGgtatttgtttgtgcatttcaagctatactggatagaattatcttttgtagtgccttcaattgatgaagcctaacttaaattctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT