Database of mouse olfactory receptor genes and cDNAs

This olfactory receptor (OR) gene database contains information about mouse OR genes, such as their sequences, map positions, ESTs and orthologous relationships to human genes. This information supplements our papers Young et al, 2003 (Genome Biology 4, R71) and Young et al, 2002 (Human Molecular Genetics 11, 535-546). Our description of the mouse OR gene family is based on analyses of the whole genome shotgun sequence produced by Celera Genomics, combined with our own phylogenetic analyses, FISH mapping of end-sequenced OR-containing BACs, and collection of mouse olfactory epithelium cDNAs. Further information about human OR genes can be obtained from HORDE.

NEW October 2003: The sequences of the cDNAs from our mouse OR screen are now available.

Release 12 OR gene data
Our web site previous to August 2003 showed information about OR genes based on Celera's release 12 of the mouse genome, and our 2002 paper refers to this dataset. The old dataset can be searched here.

Currently we provide human-mouse orthology information only for the release 12 dataset. Please contact us if you're interested in updated orthology information.

Search for information about mouse OR genes (in Celera's mouse genome release 13) by:

• gene name
• chromosome
• scaffold
• genomic location
• show information about all mouse OR genes
• show all mouse OR gene DNA or protein sequences
  
  
• show information about all cDNAs
• show all cDNA sequences

Search for BACs by:

• scaffold
• genomic location
• show all BACs

General information about the search results

1. Search results can be displayed as web page tables or as semicolon-delimited text (use File -> Save As to download and view later with spreadsheet software).

   Columns in gene tables:

2. Mouse OR gene names consist of the name of the Celera scaffold they are on, together with the start and end positions of the gene on that scaffold. For example, gene GA_x6K02T2R7CC-81245243-81246181 starts at position 81245243 on scaffold GA_x6K02T2R7CC.
   
   
3. Release 12 gene name is the corresponding gene in our old dataset, based on Celera's release 12 of the mouse genome assembly. Names again consist of the Celera scaffold they are on, together with the start and end positions of the gene on that scaffold.
   
   
4. Sequences. In the web page table display, the Sequences column contains links to the DNA and protein sequence for a gene. In the text display, this column contains the word "available" if the DNA and protein sequences are available on this web site.
   
   Fasta files of all DNA or protein sequences can be obtained through the "show all mouse OR gene DNA or protein sequences" link above. Runs of N's in the DNA sequences represent gaps in Celera's scaffold sequence. In protein sequences, *'s are stop codons, and x's are frameshifts (in reconstructed translations of pseudogenes).
   
   
5. Aliases. Any previously annotated OR gene(s) matching the sequence with >=99% nucleotide identity over >=200 bp are given, using both their Genbank accession numbers and any other names they have. Names given by Zhang and Firestein, 2002 are also shown here.
   
   
6. Intact? This column gives information about whether the genes are intact, pseudogenes, or whether only partial sequence data is available. "Pseudogenes" are sequences containing at least one stop codon or frameshift. A few of these apparent pseudogenes are probably intact genes with sequencing errors.
   
   
7. Strand. F = gene on forward strand (with respect to scaffold sequence). R = gene on reverse strand.
   
   
8. Genomic/cytogenetic location. For mouse genes, this location is based on our FISH mapping of BACs whose end sequences match the scaffold and/or on Celera's chromosomal assignments.
   
   
9. No. of cDNAs. This lists the number of cDNAs found in our screen that match sequence within a gene's 'territory'. A gene's 'territory' is defined as starting 100 kb upstream of the start codon, or 1 kb after the previous gene upstream on the same strand (whichever is closer), and ending 1 kb downstream of the start codon.
   
   
10. No. 5' splice forms. Shows the minimum number of different 5' transcriptional isoforms observed in the cDNAs we have for that gene.
    
    
11. >1 3' splice form? For genes where we estimate the 3' UTR length for at least two cDNAs, we predict alternate polyadenylation isoforms if estimates differ by 400bp or more.
    
    
12. Expression confirmed by PCR? For a small number of genes where we did not find cDNAs we used RT-PCR or PCR of the cDNA library to confirm olfactory epithelial expression.
    
    

    Columns in cDNA tables:

13. Sequences. In the web page table display, the Sequences column contains links to the DNA sequence for a cDNA. In the text display, this column contains the word "available".
    
    
14. Gene. If the cDNA sequence matches within a gene's territory (see No. of cDNAs above) then the gene name is given. cDNA sequences marked OR_unknown are from an OR gene but we cannot unambiguously determine which OR they match. Using our low stringency hybridization conditions, we also obtained sequences from a number of non-OR genes, shown at the bottom of the cDNA table.
    
    
15. Starts within ORF? Not all cDNAs in the library are full-length. Clones starting within the open reading frame are indicated here.
    
    
16. 5' UTR length is given if the sequence we obtained shows the location of the start codon in the clone.
    
    
17. 3' UTR length. Mostly very crude estimates (+/- 200 bp), a few accurate (noted).
    
    
18. cDNA end. The library was directionally cloned. Most sequences we obtained were from the 5' end of the clones, but a few were from the 3' end.
    
    
19. Other end sequence. Where a clone has been sequenced from both ends the name of the sequence from the other end of the insert is given here.
    
    
20. Comments. Our paper describes some unusual transcripts, noted here. We also list the comment "reverse strand cDNA" for clones where it appears directional cloning failed.
    
    

    Columns in BAC tables:

21. Scaffold. The scaffold the BAC's end sequences match are listed here.
    
    
22. Genomic location. The genomic location(s) found by FISH using the BAC as a probe. A few BACs FISH to several locations and are likely to contain duplicated sequence.

Updates. Information about changes made to the database can be found found here.

If you have any comments or suggestions for the improvement of this resource please contact Eleanor Williams.