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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttattatgatttgaaactactcatgtcatttattttttttaaaaagagactatttgttatttctaccatttctaaaatagtgaaattatgaaagg...

Basic information

species Oryza sativa
transcript LOC_Os01g37832.3
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g37832.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G090647_T04 (Zea mays), 5'ss of exon 7
AACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaag--ttattatgatttgaaactactca-tgtcatttattttttttaaaaagagactatttgttatttctaccatttctaaaatagtgaaattatgaaagg
|||||||||||||| || || |||||||| |||||| | ||||| ||||| ||||||||||||||||  || |||| |||   | ||||| | |||     ||    | ||  |  ||   | |||        |   ||| |||    ||   |     | || 
AACAAAAGGGATGTAGTTGCAACAATTGTATATGAAGTCATGCCCAATCCTTCTGATCACAAgtaagctttgttataatt--gatctacttaatgtttcacatcaagtctactagtagtacagttgcacaagggaaattttataatgctgtatgacctaaatag-

upper sequence: LOC_Os01g37832.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA13G29400.1 (Glycine max), 5'ss of exon 8
AACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttattatgatttgaaactactcatgtcatttattttttttaaaaagagactatttgttatt--tctaccatttctaaaatagtgaaattatgaaagg
   |||||||||||||| ||||| ||||| |||||  | ||||| ||||| ||||| |||||||||||  | |    |||  | || | || |  ||  ||  ||||   |      |   ||  |||  | ||   | | |  |  |  ||   ||  ||   
TTGAAAAGGGATGTTGTTGCCACTATTGTTTATGAGCTTATGCCAAATCCTTCTGACCACAAgtaagtattgaactcttggcattatt-atattgttagttgatttttttatatccttcaatgccattcatttatgttgtgtgcatcaaggaggctagcaagt-

upper sequence: LOC_Os01g37832.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv04s0008g00760.t01 (Vitis vinifera), 5'ss of exon 8
AACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttattat--gattt---gaaactactcatgtcatttattt--tttttaaaaagagactatttgttatttctaccatttctaaaatagtgaaattatgaaagg
   ||  |||||||||| || ||||| ||||||||||| |  || ||||| ||||||||||||||||| ||| |  |  ||   |  |    |       || | ||  | || || ||  |   ||||||    |  | |||   | |  |  | | || |||     
TTGAAGCGGGATGTTGTTGCAACAATCGTGTATGAAATTACTCCAAATCCTTCTGATCACAAgtaagtcattgtttgccttcatgggatggttttgaatgttcagttgctcttcaacaattgttgatttgt--gcttaaacatacattagttctttacatcatg-----

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|9884566|gb|BE607399.1|BE607399
EST:     TATGAAATAATGCCNTAATCCATCTGATCACAA                         AACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
genomic: TATGAAATAATGCC-TAATCCATCTGATCACAAgtaagttatt ... tgtgatgcagAACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
EST: gi|88852617|gb|CI008810.1|CI008810
EST:     GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAA                         AACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
genomic: GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttatt ... tgtgatgcagAACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
EST: gi|58678373|gb|CK067060.1|CK067060
EST:     GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAA                         AACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
genomic: GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttatt ... tgtgatgcagAACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
EST: gi|218502566|gb|FG947236.1|FG947236
EST:     GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAA                         AACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
genomic: GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttatt ... tgtgatgcagAACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
EST: gi|88269573|gb|CI380871.1|CI380871
EST:     GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAA                         AACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
genomic: GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttatt ... tgtgatgcagAACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
EST: gi|88366636|gb|CI556420.1|CI556420
EST:     GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAA                         AACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
genomic: GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttatt ... tgtgatgcagAACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
EST: gi|40724664|gb|CK431262.1|CK431262
EST:     GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAA                         AACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
genomic: GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttatt ... tgtgatgcagAACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
EST: gi|88445780|gb|CI546917.1|CI546917
EST:     GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAA                         AACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
genomic: GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttatt ... tgtgatgcagAACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
EST: gi|58594516|gb|CF992824.1|CF992824
EST:     GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAA                         AACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
genomic: GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttatt ... tgtgatgcagAACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
EST: gi|87030834|gb|CI362048.1|CI362048
EST:     GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAA                         AACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
genomic: GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttatt ... tgtgatgcagAACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
EST: gi|88831856|gb|CI369538.1|CI369538
EST:     GTTTTGGCCACAATTGTTTATGAAATAATGCCTAATCCATCTGATCACAA                         AACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA
genomic: GTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttatt ... tgtgatgcagAACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttattatgatttgaaactactcatgtcatttattttttttaaaaagagactatttgttatttctaccatttctaaaatagtgaaattatgaaagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaga