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

TATTACAAACTCAGATTACCACTATACGAACAAAATGATGAATCATGCATTCAATCGCTTCCTTCCTAATGATATGGCATGGAGAGATCTGTTTGAAATGgtgagtaatcaagttgctggttctagattgaactgtttgtcattcgttgcttgcctgccatgctgaaaactttactaagatcacttgatttattcttactgtag

Basic information

species Oryza sativa
transcript LOC_Os01g14810.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14810.3 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G044819_T02 (Zea mays), 5'ss of exon 9
TATTACAAACTCAGATTACCACTATACGAACAAAATGATGAATCATGCATTCAATCGCTTCCTTCCTAATGATATGGCATGGAGAGATCTGTTTGAAATGgtgagtaatcaagt--------tgctggttct--agattgaactgtttgtcattcgttgcttgcctgccatgctgaaaactttactaagatcacttgatttattcttactgtag
 ||||| || ||||||| ||| ||||| |||||||||||||||||||||||||||||||| |||||||||||| ||| |||||||||||||||||||||||| |||  | |  |        | |  ||| |  |||     ||||||| || || |||||| |    ||  ||| |||||| | ||| |||  || |||  || ||||| |||
CATTACTAATTCAGATTTCCATTATACAAACAAAATGATGAATCATGCATTCAATCGCTTTCTTCCTAATGATGTGGGATGGAGAGATCTGTTTGAAATGgtaagtttttatctctcccttataccagttttgtagaagtgtctgtttggcagtcattgcttac--aacacactggaaacttcattaatatccattaattc-tttttactatag

upper sequence: LOC_Os01g14810.3 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA15G21240.1 (Glycine max), 5'ss of exon 9
TATTACAAACTCAGATTACCACTATACGAACAAAATGATGAATCATGCATTCAATCGCTTCCTTCCTAATGATATGGCATGGAGAGATCTGTTTGAAATGgtgagtaatcaagttgctggttctagattgaactgtttgtcattcgttgcttgcctgccatgctgaaaactttactaagatcacttgatttattcttactgtag-----------------------------------------
|||||| ||||||||||| || |||||  ||||||||||| ||||| |||||||| | |||||||| ||||| ||||  ||||||||| | ||||| || || |||  ||   |||  | |  |  ||  ||      || || |  |   |   ||      |||||| |  | |   || | |   |||| | ||  || |                                          
TATTACCAACTCAGATTATCATTATACACACAAAATGATGCATCATTCATTCAATAGATTCCTTCCCAATGACATGGGTTGGAGAGATTTATTTGACATTgtaagt--tc---ttgtagataatcaatacaatatgaagttatcctcttgatag-tggaggaatgaaaaataca-tgctattattctctttactttttgtgaaataagcaatgcacaaattgatgtggctctcgttcatgagtag

upper sequence: LOC_Os01g14810.3 (Oryza sativa), 5'ss of exon 10
lower sequence: AT5G48960.1 (Arabidopsis thaliana), 5'ss of exon 10
TATTACAAACTCAGATTACCACTATACGAACAAAATGATGAATCATGCATTCAATCGCTTCCTTCCTAATGATATGGCATGGAGAGATCTGTTTGAAATGgtgagtaatcaagttgctggttctagattg-aactgtttgtcattcgttgctt---gcctgccatgctgaaaactttactaagatcacttgatttattcttac-tgtag
||| |||||||| ||||| ||||| ||  ||||||||||||| ||| |||| ||    |||||||| ||||| ||||  ||| ||||||| ||||| |||||||| || |       || ||||  |||   | |||   ||  | |||  |    |  |    |||   | ||||||||    |   |  ||| ||  || |   |||
TATCACAAACTCGGATTATCACTACACAGACAAAATGATGAAGCATTCATTTAACAAATTCCTTCCCAATGACATGGACTGGCGAGATCTTTTTGACATGgtgagcaaacgtaaatttgtttctgcattttgattgtaaatctgttgtttttcagagagtagtttgcattagactttactg---tttttgaattcatgtttccacatag

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|29627736|gb|CB632747.1|CB632747
EST:     TCAATCGCTTCCTTCCTAATGATATGGCATGGAGAGATCTGTTTGAAATG                         GTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTA
genomic: TCAATCGCTTCCTTCCTAATGATATGGCATGGAGAGATCTGTTTGAAATGgtgagtaatc ... cttactgtagGTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTA
EST: gi|29673384|gb|CB669659.1|CB669659
EST:     TCAATCGCTTCCTTCCTAATGATATGGCATGGAGAGATCTGTTTGAAATG                         GTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTA
genomic: TCAATCGCTTCCTTCCTAATGATATGGCATGGAGAGATCTGTTTGAAATGgtgagtaatc ... cttactgtagGTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTACAAACTCAGATTACCACTATACGAACAAAATGATGAATCATGCATTCAATCGCTTCCTTCCTAATGATATGGCATGGAGAGATCTGTTTGAAATGgtgagtaatcaagttgctggttctagattgaactgtttgtcattcgttgcttgcctgccatgctgaaaactttactaagatcacttgatttattcttactgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC