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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag

Basic information

species Oryza sativa
transcript LOC_Os01g23610.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 10
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag
||||| ||||| |||||||| |||||||||||||| || |||||||| |||||||| ||||| ||||||||||||||||||| ||         | || ||||   ||| || ||        |||  |    | |         |  | | ||||||||  |  |  || |  | ||||||||||||
GTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAGgtaaatgt-------tgtgctcacctgtttcttttatc------catgctcgatgct--------gatcactatagttcttatacgagcaaatgttggtctgaatatag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 10
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag
|| ||  |||| ||||||||||| ||||| ||||||||  | ||||| |||||||||||||||||||||||||| |||||||  |    | | || |         |||     | || ||   ||    |    | |  |||||  |     | || | | | |                       
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactgatgta------acttttccaaaatttagtttatgcagcaa--tatcatttga--tgaaaaaattgtctaacag----------------------

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 5
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag
|||||  |||||||||| ||||| ||| | ||||||||  | ||||| |||||||||||||||||||||||||| |||||||   |   | |||| |    | | |  || |    ||     ||| |       ||  |||      | | | ||| || || |                       
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaagtaatgta---attttgctactaatatttgagtcatttgcttccattcacttaatgaaaatattgttgttggaaag----------------------

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA15G15310.1 (Glycine max), 5'ss of exon 10
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag
|||||  |||||||||||||||| ||||| ||||||||  | ||||| |||||||||||||| ||||||||||| |||||||   |     |||| |    | | |  || |    ||     ||| |       ||| |||   | |       || || ||||                       
GTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAGgtaagaagcaggtaatgta---attttgctactaatttttgagtcatttgcttccatttactt---aatgaaaagattgttggatag----------------------

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA07G37050.1 (Glycine max), 5'ss of exon 10
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag
|| ||  |||| || |||||||| ||||| ||||||||  | ||||| |||||||||||||||||||||||||| |||||||  |      ||| |  |  | | ||       | || ||    |  | |    | |  |||||  |     | || | | | |                       
GTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtg----gtaactcatgtaattttcccaaaaattttagtttttgctgcaa--tatcatttga--tgaaaaaattgtctaacag----------------------

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagata-cagaataatttgttcactgttttattgta-cttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag---------
|||||  | ||||| || || || ||||||||||| ||||| ||||| |||||||| || ||||| |||||||| || |||| ||      || | |  |||||  |   | || | |||       | ||||   || | |  ||||   ||    ||      ||   || |   ||  |  |  |           
GTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTGgtaaatggttttatcaatatttcac--tccaaatgcatctttcttttgtttttccttttctacactgaatacgttagattgacctttattaaactctatgcatctacttgtgttggctag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 5'ss of exon 10
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag
||||| || ||||| || ||||| ||||||||||| ||| | ||||| || ||||| |||||||| |||||||| || |||| ||     || | | |    ||  |  |   | |   |     |        || | |||    || || |    || |||   || | |   || ||        
GTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTGgtaaatggcttatcagtaggaggctacta-acaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctag------

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 10
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag
|||||  | |||||||| || || ||||| ||||| ||| | ||||| |||||||| || |||||||||||||| ||||||   |      ||| |   ||| | ||||  |||  |       |  |||     |     || ||| |   |  || ||||    ||    ||||||    ||  ||
GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtg----gtaactacctca-tattttgctgtttt-------acctttaaaaatgctacttaaaccatcttcattttttg----cttggctcttgt---gatgcag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 5'ss of exon 10
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctg--aatatag
|||||  | |||||||| ||||| ||||| ||||| ||| | ||||| ||||||||||| ||||| ||||||||||| ||||  |||    |  ||||||  |  | |   | |||| ||  |  | | ||   ||  | ||| |       ||  |  |||| | || | || |  | ||   | ||||
GTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTGgtaattacc---ttgtttgttgccactctctctctactacatggtttttgtca--ttcagttttaa-------tatctacttgaaacctgacttttcttttgtcgacatag

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ06739 (Selaginella moellendorffii), 5'ss of exon 10
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatac-agaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag
|| ||  ||||||| || || || ||||| ||||||||||| ||||| ||||| ||||||||||| || || || |||||||    | |||   |  ||||   ||   |  |||      |  | | | ||   ||||||                                                
GTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGgtaatctcgagagagacatgttttgtg---tgatgtgaccgtgatcgtgtctc---ttttgcag----------------------------------------------

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ16882 (Selaginella moellendorffii), 5'ss of exon 10
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatac-agaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag
|| ||  ||||||| || || || ||||| ||||||||||| ||||| ||||| ||||||||||| || || || |||||||    | |||  ||  ||||   ||| | || ||      |  | | | ||   ||||||                                                
GTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGgtaatctcgagagaaacatgtt--ttgtatgat-gtgaccgtgatcgtgtctc---ttttgcag----------------------------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag

- - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA