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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcgacctgctcttcagatgttccgtaagagtgtttcacatggcgtctctgaagttttagctaataaattttgtttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGATACCCCTGAAGGGAAGAAACTTTTTCTTGTTGATCTTGGACTAG

Basic information

species Oryza sativa
transcript LOC_Os01g10150.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 6
gtaactcgac--ctgctcttcagatgttccgtaagagtgtttcacatggcgtctctgaagttttagctaataaattttgtttatgaca--gGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGATACCCCTGAAGGGAAGAAACTTTTTCTTGTTGATCTTGGACTAG
|| |   |    ||| | || |||||   | |     | | | | ||||    | | ||  |  | || ||||  |  || |||||||  |||| ||||||||||||||||| ||||||||||| |||||||||||||| | |||||| || | |||||| |||||||||||||| |||||| | |
gtgatctgctttctgttgttgagatggaactt---tttttcttatatggttgttttaaaagtggatctcataagatgcgtatatgacacagGTATGTCCATGGTGATGTGAAGCCTGAGAACTTCTTGCTTGGTCCTCCTGGTACCCCAGAGGAGAAGAAGCTTTTTCTTGTTGACCTTGGATTGG

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 6
------------gtaactcgacctgctcttcagatgttccgtaagagtgtttcacatg-gcgtctctgaagttttagctaataaattttgtttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGATACCCCTGAAGGGAAGAAACTTTTTCTTGTTGATCTTGGACTAG
            |||  | || |       || |    |    | |    |  | ||     | | |  | ||  || ||  |   | |  ||||  ||| || || || |||||||| ||||||||||||||||||||||| |  || |  || | ||| |  |||||  | ||||| |||||||||||| |||
gatggattgttggtatattgatcgcacacacacacacacacacacacacatatatatatatatatatatatttcaagttagaatggtgtcattattgcagATATGTACACGGTGATGTAAAACCTGAGAACTTTTTGCTTGGACTCCCTGGAACTCTTGATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 6
----------gtaactcgacctgctcttcagat-gttccgtaagagtgtt-tcacatggcgtctctgaagt-tttagctaataaattttgtttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGATACCCCTGAAGGGAAGAAACTTTTTCTTGTTGATCTTGGACTAG
          ||| |   | | |||     ||| ||||  |    || |  ||||||  |||  |   |   |||      ||   | |  |||| |||| || || || |||||||| ||||||||||||||||||||||| || || |  || ||| | |  |||||  | ||||| |||||||||||| |||
agttagcatggtatcagcagcagctacatggattgttcatttttggtatgatcacatttcgttgcaagaacatttcatctttatgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTTGGACCCCCTGGAACTCCTAATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 6
-------gtaactcgacctgctcttcagatgttccgtaagagtgtt-----tcacatggcgtctctgaagt-tttagctaataaattttgtttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGATACCCCTGAAGGGAAGAAACTTTTTCTTGTTGATCTTGGACTAG
        || |  |   |  || |||| |     |   | |  ||     ||||||   ||  |   | | |||    | |    | |  |||| |||| || || || |||||||| |||||||||||||||||||| || || || |  || ||||| |  |||||  | ||||| |||||||||||| |||
atgtaagttagcatggtatcatcatcagctacatggattgtggtttattgatcacattatgttgcaagaatatttcatcattctgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTGGGACCCCCTGGAACTCCTGATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 6
gtaactcgacctgctcttcagatgttccgtaagagtgtttcacatggcgtctctgaa---gttttagc-------taataaattttgt---ttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGATACCCCTGAAGGGAAGAAACTTTTTCTTGTTGATCTTGGACTAG
                                         | |           ||   | | |||        |||| | |  ||    || || |||||| || ||||| ||||| || ||||||||||||||||||||||||||||  ||   ||| | ||| ||||| ||||||||||| |||||| |||
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaaaaaaaaaaaaaaaaagatatagtgctgttataatgactcctgcaacttctggcagGTATGTGCATGGGGATGTAAAGCCTGAGAACTTTTTGCTTGGTCCTCCAGGAACTAATGAGGAGAAAAAACTGTTTCTTGTTGACCTTGGATTAG

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 6
-----gtaactcgacctgctcttcagatgttccgtaag--agtgtttcaca-----tggcgtct-ctgaagttttagctaataaattttgtttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGATACCCCTGAAGGGAAGAAACTTTTTCTTGTTGATCTTGGACTAG
     | || |  |     || || | |     | ||   |||||||         ||   | |  ||   || ||    || |       || || |||||| || ||||||||||| || ||||| |||||  ||||||||||||| |  ||  |||| | ||| ||| | ||||||||||||||||| ||||
atcctgcaaatgcattatttcctctgttcagatgcaatctagtgttttgagatctttgaaatatattgcccttatattggatgatcacaacttttggcagGTATGTGCATGGTGATGTCAAGCCTGAAAACTTCCTGCTTGGTCCTCCGGGAACGGCTGATGAGAAAAAATTATTTCTTGTTGATCTTGGGCTAG

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|29688778|gb|CB685053.1|CB685053
EST:     TGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGG                         GTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGA
genomic: TGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGGgtaactcgac ... tttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGA
EST: gi|29630440|gb|CB635449.1|CB635449
EST:     TGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGG                         GTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCT
genomic: TGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGGgtaactcgac ... tttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCT
EST: gi|88573975|gb|CI665744.1|CI665744
EST:     TGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGG                         GTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGA
genomic: TGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGGgtaactcgac ... tttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGA
EST: gi|29645031|gb|CB650038.1|CB650038
EST:     TGTATAGGTATCCTTGCCATCTCCATACTAGAGAAGATGCATGCTAAAGG                         GTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGA
genomic: TGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGGgtaactcgac ... tttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtgtttcacatggcgtctctgaagttttagctaataaattttgtttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGATACCCCTGAAGGGAAGAAACTTTTTCTTGTTGATCTTGGACTAG
                              agctaat  putative branch site (score: 3)
                                        ttttgttt  putative PPT
                       aagttttagctaataa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactcgacctgctcttcagatgttccgtaagagtgtttcacatggcgtctctgaagttttagctaataaattttgtttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGATACCCCTGAAGGGAAGAAACTTTTTCTTGTTGATCTTGGACTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA