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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_Os01g37832.1
intron # 8
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 62 (upstream exon), 72 (downstream exon)
Score: 64

AACAAAAGGGATGTTGTGGCCACAATTGTGTATGAAATAATGCCTAATCCATCTGATCACAAgtaagttatt ... tgtgatgcagAACTAAGTCTGAGACTGGAGGTGGTTTCTCGCATGTTGAGTAGGCATGTCAG




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