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Table 2 Summary of all candidate genes.

From: Rgcs1, a dominant QTL that affects retinal ganglion cell death after optic nerve crush in mice

Gene Name Chromosome Position
(starting bp)
Retinal Expression Coding Region SNPc Strain Associationd Role in Neurodegeneration
Pcdh7 58006337 GCL enricheda,b No N/A Unknown
Tlr1 65203969 Confirmedb Yes Possible Immune Modulatione
Tlr6 65232241 Confirmedb Yes Yes Immune Modulatione
Uchl1 66955376 GCL enricheda,b No N/A eQTL Susceptibility Allelef
Sparcl1 104319413 GCL enricheda,b Yes Possible Possible Glial Activationg
Cplx1 108760431 GCL enricheda,b No N/A 2° Degenerationh
Hspb8 116669490 Confirmedb No N/A Susceptibility Allelei
  1. The chromosomal position of each gene is shown, along with a short summary of how each gene scored in the different criteria for identifying candidate genes.
  2. aIdentified from microarray expression profiles.
  3. bThe expression of each candidate gene was confirmed in the mouse retina using reverse transcriptase-PCR amplification of a portion of its cDNA (data not shown).
  4. cSingle nucleotide polymorphism (SNP) analysis was conducted in silico using sequence information available on the MGI data base. SNPs that resulted in coding region changes between DBA/2J and BALB/cByJ mice were examined.
  5. dCoding region SNPs between DBA/2J and BALB/cByJ mice were compared to reference strains if sequence data were available. Reference strains included 129X1/SVJ and C57Bl/6J as resistant strains comparable to DBA/2J mice, and NOD/LtJ and C3H/HeJ as susceptible strains comparable to BALB/cByJ mice. Intermediate strains included A/J (as a likely resistant strain) and NZB/BINJ (as a likely susceptible strain). For genes showing a SNP difference, if the same SNP was noted in the reference strains it was scored as showing a positive strain association. A possible strain association was recorded if sequence data was limited to only a resistant or susceptible reference strain, or the intermediate strains showed the predicted strain association, but there was not data available for the reference strains. If no SNP was noted, the strain association analysis was not applicable (N/A).
  6. e[31, 33].
  7. f [3436].
  8. g[37].
  9. h[40].
  10. i[45]