Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaggaaattatttggagtcgaaagtgctctcgctagctagttactgctttactctgcactaatatgaatttgaaactgatgatttgatcaatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTGGCATCCTTTTACGAACGTGCTGGTAAGGTGAAATGTCTCGGCAGTCCAG

Basic information

species Oryza sativa
transcript LOC_Os06g45120.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 13
----------------------------------------------------actaggaaatt--atttggagtcgaaagtgctctcgctagctagttactgctttactctgcacta-----atatgaat-----ttga--aac------tgatgatttgatcaatttcca--gGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTGGCATCCTTTTACGAACGTGCTGGTAAGGTGAAATGTCTCGGCAGTCCAG
                                                      || || |||  | ||    ||   | |  | |  ||||  | ||  |     | |  |||  |     ||  ||||     ||||  ||       ||||||| |  |    |||||  ||| ||||||||||| |||||||| || ||||||||  | ||||||||||| || || || || ||||||||||| ||||| |||||||| ||  | || |
gtgagaaagatttattttttgtgcttaaaatacatatattttgtagccttactttatgatattgaactttctttcttgactagtttaactagacaatttatataccattaggcatgagacacatgggaatggacattgatcaatgtattttgatgatattgttgtcttccacagGCAGAAATGCCTGCAGATAGTGGATATCCTGCATACCTTGCTGCACGTTTAGCCTCTTTCTATGAACGTGCTGGGAAGGTAAAATGTCTAGGAGGCCCTG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 13
actaggaaattatttggagtcgaaagtgctctcgctagctagttactgctttactctgcactaatatgaatttgaaactgatgatttgatcaatttcca--gGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTGGCATCCTTTTACGAACGTGCTGGTAAGGTGAAATGTCTCGGCAGTCCAG
 || |   | | |    || | |      |  |  || | |       | |     || ||    || ||| | |   |||||||    |    |||||  ||| ||||||||||| |||||||| || ||||||||  | ||||||||||| || || || || ||||||||||| ||||| |||||||| ||  | || |
-cttgactagtgtaactagacaatttatataccattaaccatgagacacatgggaatggacattgatcaatgt-attttgatgatgctgttgtcttccacagGCAGAAATGCCTGCAGATAGTGGATATCCTGCATACCTTGCTGCACGTTTAGCCTCGTTCTATGAACGTGCTGGGAAGGTAAAATGTCTTGGAGGCCCTG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
-----actaggaaatta--tttggagtcgaaagtgctctcgctagctagttactgctttactctgcactaatatgaatttgaaactgatgatttgatcaatttc-cagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTGGCATCCTTTTACGAACGTGCTGGTAAGGTGAAATGTCTCGGCAGTCCAG
       || |   ||   ||| |         || ||  | |  |    |    |||| || |     | | |    |||| ||  ||  |||| |   |||   |||||||||||||||| || ||||| || || || ||| | || |||||||| ||||| || || |||||||||||||| || |||||||| ||  | ||||
gtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctttttctcagttta---ttgacacctat--tttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 13
----actaggaaattatttggagtcgaaag--tgctctcgctagctagttactgctttactctgcactaatatgaat-ttgaaactgatgatttgatcaatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTGGCATCCTTTTACGAACGTGCTGGTAAGGTGAAATGTCTCGGCAGTCCAG
      |   | || | |     | ||||   || | | |  | ||    |  |  |  || |||  || | ||||  |||| |   || ||||  | |||   ||||| |||||||| || || |||||||||||||| ||| |||| |||||||| || || || || || ||||||||||| || || || || ||  | ||||
gcatgatttcatataactgcattttgaaatattgattttgtaatctga--agcgtgtctctttgc-ttactctgaaaattgacaactataatttc-ttaat---cagGCAGAAATGCCAGCAGACAGTGGTTACCCTGCTTATCTGGCAGCACGTTTAGCCTCTTTCTATGAGCGTGCTGGTAAAGTTAAGTGCCTTGGTGGGCCAG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 13
actaggaaattatttgg--agtcgaaagtgctctcgctagctagttactgct-ttactctgcactaatatgaatttgaaactgatgatttgatcaatttcca-gGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTGGCATCCTTTTACGAACGTGCTGGTAAGGTGAAATGTCTCGGCAGTCCAG
  ||   | ||||||    | | |||       |   |||| | |||  | | ||| ||  | ||    |  | |  ||  |  ||  || ||   |    | |||||| ||||||||||||||||| || ||||| |||||||| |||||||| || || || || || || ||||| || ||||||||||| ||  | ||||
--tatttatttatttatttatttgaatcattattatttagcaatttagggttattattcatctctggctt--actccaatattttgtcttaatttctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTAGCCTCTTTCTATGAGCGCGCTGGCAAAGTGAAATGTCTGGGTGGACCAG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 12
actaggaaattatttggagtcgaaagtgctctcgctagctagttactgctttactctgcactaatatgaatttgaaactgatgatttgatcaatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTGGCATCCTTTTACGAACGTGCTGGTAAGGTGAAATGTCTCGGCAGTCCAG
                                     |  |||  ||| ||| || |   ||| |   |||||  ||  |  |              ||||| ||||||||||| || |||||||| || || ||||||| ||||||||||||  | |||||||| || ||||| ||||| ||||| || || ||||| |
-------------------------------------gtaagtctctgattttcttt---ctattcctaatttacaaacgccg------------cgcagGCCGAAATGCCTGCCGACAGTGGTTATCCAGCGTATTTGGGTGCACGTTTGGCTACGTTTTACGAGCGGGCTGGAAAGGTTAAATGCCTTGGTAGTCCCG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 13
actaggaaattatttggagtcgaaagtgctctcgctagctagttactgctttactctgcactaatatgaatttgaaactgatgatttgatcaatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTGGCATCCTTTTACGAACGTGCTGGTAAGGTGAAATGTCTCGGCAGTCCAG
                                     |  |||  ||| ||| || |   ||| |   |||||  ||  |  |              ||||| ||||||||||| || |||||||| || || ||| ||| ||||||||||||  | |||||||| || ||||| ||||| ||||| || || ||||| |
-------------------------------------gtaagtctctgattttcttt---ctattcctaatttacaaacgccg------------cgcagGCCGAAATGCCTGCCGACAGTGGTTATCCAGCGTATCTGGGTGCACGTTTGGCTACGTTTTACGAGCGGGCTGGAAAGGTTAAATGCCTTGGTAGTCCCG

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|58692820|gb|CK081507.1|CK081507
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|58611693|gb|CK039405.1|CK039405
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|58659487|gb|CK048167.1|CK048167
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCC
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCC
EST: gi|33804193|gb|CF327971.1|CF327971
EST:     CGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: CGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|116875037|gb|EC365545.1|EC365545
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|66919084|gb|CX105932.1|CX105932
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|116875538|gb|EC366046.1|EC366046
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|58657888|gb|CK046568.1|CK046568
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGGGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|29617005|gb|CB622017.1|CB622017
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|27578142|gb|CB000837.1|CB000837
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
EST: gi|58594482|gb|CF992790.1|CF992790
EST:     ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTG                         GCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG
genomic: ATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgct ... caatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctttactctgcactaatatgaatttgaaactgatgatttgatcaatttccagGCTGAAATGCCTGCGGATAGTGGTTACCCTGCATATTTGGCTGCACGTTTGGCATCCTTTTACGAACGTGCTGGTAAGGTGAAATGTCTCGGCAGTCCAG
                                                tttcc  CT-rich tract
                taatatgaatttgaaa  TA-rich tract