Arrd1 QTL Detail

Summary

• Symbol
  Arrd1
• Name
  age-related retinal degeneration 1

• Feature Type
  QTL
• IDs
  MGI:2664137
  NCBI Gene: 492874
• Candidate Genes
  7 Genes

Location &
Maps

• Sequence Map
  Chr6:75521339-92584431 bp

  From MGI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 6, cM position of peak correlated region/marker: Syntenic
• Mapping Data
  2 experiments

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  1 phenotype from 2 alleles in 1 genetic background
  1 phenotype reference
  

• All Mutations and Alleles
  2
• QTL
  2
• Incidental Mutations
  APF
• Find Mice (IMSR)
  0 strains or lines available

Sequences &
Gene Models

• NCBI Gene
  492874

References

• Summaries
  All 4

  Phenotypes 1
• Earliest
  J:83546 Danciger M, et al., A strong and highly significant QTL on chromosome 6 that protects the mouse from age-related retinal degeneration. Invest Ophthalmol Vis Sci. 2003 Jun;44(6):2442-9
• Latest
  J:166304 Ogando DG, et al., Candidate genes for chromosomes 6 and 10 quantitative trait loci for age-related retinal degeneration in mice. Mol Vis. 2010;16:1004-18

Candidate Genes for Arrd1:

Gene	Genome Location (GRCm39)	Reference	QTL Note
Aplf	Chr6:87605406-87649175 (-)	J:118199	Linkage analysis was performed on 170 animals from a (A/J x C57BL/6J)F2 intercross to determine if age-related retinal degeneration QTLs previously identified in a (C57BL/6J-Tyr x BALB/cByJ)F2 intercross are present. Parental strain A/J exhibits greater age-related retinal degeneration compared to C57BL/6J. F2 animals were maintained in a dimly-lit environment and sacrificed at 8 months of age. The retinal outer nuclear layer was recorded for each animal. Eighty-six polymorphic markers at an average spacing of 13.1 cM were used for the genome scan. Previously identified QTLs Arrd1 (chr6), Arrd2 (chr10), and Arrd3 (chr16) were not detected in this cross. However, SNP analysis was used to identify positional candidate genes for Arrd1 at 35 cM. Prokr1, Gkn1, Gata2 (38.5 cM) , 2010301N04Rik, and E230015B07Rik map to the Arrd1 interval and are expressed in the eye. Antxr, Ruvbl1, and Eefsec map to the Arrd1 locus but do not exhibit co-expression with retina- or RPE-specific genes. Significant linkage to age-related retinal degeneration was detected on the X chromosome between DXMit192 (16 cM) and DXMit19 (43.2 cM). This locus is named Arrd4 (age-related retinal degeneration 4). Males hemizygous for C57BL/6J-derived alleles at Arrd4 exhibit decreased retinal degeneration compared to females with A/J-derived alleles. Thus, Arrd4 appears to have a sex-dependent effect. Suggestive linkage to age-related retinal degeneration mapped to proximal mouse Chromosome 14 between D14Mit98 (3 cM) and D14Mit60 (15 cM) with LOD=2.15. This region overlaps with a suggestive locus detected in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross. C57BL/6J-derived alleles confer susceptibility retinal degeneration in both crosses. Suggestive linkage was detected at 13 cM- 29 cM on mouse Chromosome 12 between D12Mit59 and D12Mit91 (LOD=2.24). This locus was also suggestive in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross between D12Mit60 (16 cM) and D12Mit236 (22 cM). C57BL/6J-derived alleles confer susceptibility to retinal degeneration in both crosses. A distal locus also shows suggestive linkage to retinal degeneration in (A/J x C57BL/6J)F2 animals at 53 cM - 59 cM (LOD=2.91). C57BL/6J-derived alleles at this locus confers susceptibility to retinal degeneration. Suggestive linkage unique to the (A/J x C57BL/6J)F2 cross mapped to 35 cM (D13Mit13) - 40 cM (D13Mit256) on mouse Chromosome 13 (LOD=2.85) and 22.9 cM (D17Mit51) - 34.3 cM (D17Mit20) on mouse Chromosome 17 (LOD=2.22). C57BL/6J-derived alleles at these loci confer resistance to age-related retinal degeneration.
E230015B07Rik	Chr6:87648965-87653318 (+)	J:118199	Linkage analysis was performed on 170 animals from a (A/J x C57BL/6J)F2 intercross to determine if age-related retinal degeneration QTLs previously identified in a (C57BL/6J-Tyr x BALB/cByJ)F2 intercross are present. Parental strain A/J exhibits greater age-related retinal degeneration compared to C57BL/6J. F2 animals were maintained in a dimly-lit environment and sacrificed at 8 months of age. The retinal outer nuclear layer was recorded for each animal. Eighty-six polymorphic markers at an average spacing of 13.1 cM were used for the genome scan. Previously identified QTLs Arrd1 (chr6), Arrd2 (chr10), and Arrd3 (chr16) were not detected in this cross. However, SNP analysis was used to identify positional candidate genes for Arrd1 at 35 cM. Prokr1, Gkn1, Gata2 (38.5 cM) , 2010301N04Rik, and E230015B07Rik map to the Arrd1 interval and are expressed in the eye. Antxr, Ruvbl1, and Eefsec map to the Arrd1 locus but do not exhibit co-expression with retina- or RPE-specific genes. Significant linkage to age-related retinal degeneration was detected on the X chromosome between DXMit192 (16 cM) and DXMit19 (43.2 cM). This locus is named Arrd4 (age-related retinal degeneration 4). Males hemizygous for C57BL/6J-derived alleles at Arrd4 exhibit decreased retinal degeneration compared to females with A/J-derived alleles. Thus, Arrd4 appears to have a sex-dependent effect. Suggestive linkage to age-related retinal degeneration mapped to proximal mouse Chromosome 14 between D14Mit98 (3 cM) and D14Mit60 (15 cM) with LOD=2.15. This region overlaps with a suggestive locus detected in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross. C57BL/6J-derived alleles confer susceptibility retinal degeneration in both crosses. Suggestive linkage was detected at 13 cM- 29 cM on mouse Chromosome 12 between D12Mit59 and D12Mit91 (LOD=2.24). This locus was also suggestive in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross between D12Mit60 (16 cM) and D12Mit236 (22 cM). C57BL/6J-derived alleles confer susceptibility to retinal degeneration in both crosses. A distal locus also shows suggestive linkage to retinal degeneration in (A/J x C57BL/6J)F2 animals at 53 cM - 59 cM (LOD=2.91). C57BL/6J-derived alleles at this locus confers susceptibility to retinal degeneration. Suggestive linkage unique to the (A/J x C57BL/6J)F2 cross mapped to 35 cM (D13Mit13) - 40 cM (D13Mit256) on mouse Chromosome 13 (LOD=2.85) and 22.9 cM (D17Mit51) - 34.3 cM (D17Mit20) on mouse Chromosome 17 (LOD=2.22). C57BL/6J-derived alleles at these loci confer resistance to age-related retinal degeneration.
Eefsec	Chr6:88234318-88423489 (-)	J:118199	Linkage analysis was performed on 170 animals from a (A/J x C57BL/6J)F2 intercross to determine if age-related retinal degeneration QTLs previously identified in a (C57BL/6J-Tyr x BALB/cByJ)F2 intercross are present. Parental strain A/J exhibits greater age-related retinal degeneration compared to C57BL/6J. F2 animals were maintained in a dimly-lit environment and sacrificed at 8 months of age. The retinal outer nuclear layer was recorded for each animal. Eighty-six polymorphic markers at an average spacing of 13.1 cM were used for the genome scan. Previously identified QTLs Arrd1 (chr6), Arrd2 (chr10), and Arrd3 (chr16) were not detected in this cross. However, SNP analysis was used to identify positional candidate genes for Arrd1 at 35 cM. Prokr1, Gkn1, Gata2 (38.5 cM) , 2010301N04Rik, and E230015B07Rik map to the Arrd1 interval and are expressed in the eye. Antxr, Ruvbl1, and Eefsec map to the Arrd1 locus but do not exhibit co-expression with retina- or RPE-specific genes. Significant linkage to age-related retinal degeneration was detected on the X chromosome between DXMit192 (16 cM) and DXMit19 (43.2 cM). This locus is named Arrd4 (age-related retinal degeneration 4). Males hemizygous for C57BL/6J-derived alleles at Arrd4 exhibit decreased retinal degeneration compared to females with A/J-derived alleles. Thus, Arrd4 appears to have a sex-dependent effect. Suggestive linkage to age-related retinal degeneration mapped to proximal mouse Chromosome 14 between D14Mit98 (3 cM) and D14Mit60 (15 cM) with LOD=2.15. This region overlaps with a suggestive locus detected in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross. C57BL/6J-derived alleles confer susceptibility retinal degeneration in both crosses. Suggestive linkage was detected at 13 cM- 29 cM on mouse Chromosome 12 between D12Mit59 and D12Mit91 (LOD=2.24). This locus was also suggestive in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross between D12Mit60 (16 cM) and D12Mit236 (22 cM). C57BL/6J-derived alleles confer susceptibility to retinal degeneration in both crosses. A distal locus also shows suggestive linkage to retinal degeneration in (A/J x C57BL/6J)F2 animals at 53 cM - 59 cM (LOD=2.91). C57BL/6J-derived alleles at this locus confers susceptibility to retinal degeneration. Suggestive linkage unique to the (A/J x C57BL/6J)F2 cross mapped to 35 cM (D13Mit13) - 40 cM (D13Mit256) on mouse Chromosome 13 (LOD=2.85) and 22.9 cM (D17Mit51) - 34.3 cM (D17Mit20) on mouse Chromosome 17 (LOD=2.22). C57BL/6J-derived alleles at these loci confer resistance to age-related retinal degeneration.
Gata2	Chr6:88170873-88184014 (+)	J:118199	Linkage analysis was performed on 170 animals from a (A/J x C57BL/6J)F2 intercross to determine if age-related retinal degeneration QTLs previously identified in a (C57BL/6J-Tyr x BALB/cByJ)F2 intercross are present. Parental strain A/J exhibits greater age-related retinal degeneration compared to C57BL/6J. F2 animals were maintained in a dimly-lit environment and sacrificed at 8 months of age. The retinal outer nuclear layer was recorded for each animal. Eighty-six polymorphic markers at an average spacing of 13.1 cM were used for the genome scan. Previously identified QTLs Arrd1 (chr6), Arrd2 (chr10), and Arrd3 (chr16) were not detected in this cross. However, SNP analysis was used to identify positional candidate genes for Arrd1 at 35 cM. Prokr1, Gkn1, Gata2 (38.5 cM) , 2010301N04Rik, and E230015B07Rik map to the Arrd1 interval and are expressed in the eye. Antxr, Ruvbl1, and Eefsec map to the Arrd1 locus but do not exhibit co-expression with retina- or RPE-specific genes. Significant linkage to age-related retinal degeneration was detected on the X chromosome between DXMit192 (16 cM) and DXMit19 (43.2 cM). This locus is named Arrd4 (age-related retinal degeneration 4). Males hemizygous for C57BL/6J-derived alleles at Arrd4 exhibit decreased retinal degeneration compared to females with A/J-derived alleles. Thus, Arrd4 appears to have a sex-dependent effect. Suggestive linkage to age-related retinal degeneration mapped to proximal mouse Chromosome 14 between D14Mit98 (3 cM) and D14Mit60 (15 cM) with LOD=2.15. This region overlaps with a suggestive locus detected in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross. C57BL/6J-derived alleles confer susceptibility retinal degeneration in both crosses. Suggestive linkage was detected at 13 cM- 29 cM on mouse Chromosome 12 between D12Mit59 and D12Mit91 (LOD=2.24). This locus was also suggestive in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross between D12Mit60 (16 cM) and D12Mit236 (22 cM). C57BL/6J-derived alleles confer susceptibility to retinal degeneration in both crosses. A distal locus also shows suggestive linkage to retinal degeneration in (A/J x C57BL/6J)F2 animals at 53 cM - 59 cM (LOD=2.91). C57BL/6J-derived alleles at this locus confers susceptibility to retinal degeneration. Suggestive linkage unique to the (A/J x C57BL/6J)F2 cross mapped to 35 cM (D13Mit13) - 40 cM (D13Mit256) on mouse Chromosome 13 (LOD=2.85) and 22.9 cM (D17Mit51) - 34.3 cM (D17Mit20) on mouse Chromosome 17 (LOD=2.22). C57BL/6J-derived alleles at these loci confer resistance to age-related retinal degeneration.
Gkn1	Chr6:87322635-87327897 (-)	J:118199	Linkage analysis was performed on 170 animals from a (A/J x C57BL/6J)F2 intercross to determine if age-related retinal degeneration QTLs previously identified in a (C57BL/6J-Tyr x BALB/cByJ)F2 intercross are present. Parental strain A/J exhibits greater age-related retinal degeneration compared to C57BL/6J. F2 animals were maintained in a dimly-lit environment and sacrificed at 8 months of age. The retinal outer nuclear layer was recorded for each animal. Eighty-six polymorphic markers at an average spacing of 13.1 cM were used for the genome scan. Previously identified QTLs Arrd1 (chr6), Arrd2 (chr10), and Arrd3 (chr16) were not detected in this cross. However, SNP analysis was used to identify positional candidate genes for Arrd1 at 35 cM. Prokr1, Gkn1, Gata2 (38.5 cM) , 2010301N04Rik, and E230015B07Rik map to the Arrd1 interval and are expressed in the eye. Antxr, Ruvbl1, and Eefsec map to the Arrd1 locus but do not exhibit co-expression with retina- or RPE-specific genes. Significant linkage to age-related retinal degeneration was detected on the X chromosome between DXMit192 (16 cM) and DXMit19 (43.2 cM). This locus is named Arrd4 (age-related retinal degeneration 4). Males hemizygous for C57BL/6J-derived alleles at Arrd4 exhibit decreased retinal degeneration compared to females with A/J-derived alleles. Thus, Arrd4 appears to have a sex-dependent effect. Suggestive linkage to age-related retinal degeneration mapped to proximal mouse Chromosome 14 between D14Mit98 (3 cM) and D14Mit60 (15 cM) with LOD=2.15. This region overlaps with a suggestive locus detected in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross. C57BL/6J-derived alleles confer susceptibility retinal degeneration in both crosses. Suggestive linkage was detected at 13 cM- 29 cM on mouse Chromosome 12 between D12Mit59 and D12Mit91 (LOD=2.24). This locus was also suggestive in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross between D12Mit60 (16 cM) and D12Mit236 (22 cM). C57BL/6J-derived alleles confer susceptibility to retinal degeneration in both crosses. A distal locus also shows suggestive linkage to retinal degeneration in (A/J x C57BL/6J)F2 animals at 53 cM - 59 cM (LOD=2.91). C57BL/6J-derived alleles at this locus confers susceptibility to retinal degeneration. Suggestive linkage unique to the (A/J x C57BL/6J)F2 cross mapped to 35 cM (D13Mit13) - 40 cM (D13Mit256) on mouse Chromosome 13 (LOD=2.85) and 22.9 cM (D17Mit51) - 34.3 cM (D17Mit20) on mouse Chromosome 17 (LOD=2.22). C57BL/6J-derived alleles at these loci confer resistance to age-related retinal degeneration.
Prokr1	Chr6:87555573-87567725 (-)	J:118199	Linkage analysis was performed on 170 animals from a (A/J x C57BL/6J)F2 intercross to determine if age-related retinal degeneration QTLs previously identified in a (C57BL/6J-Tyr x BALB/cByJ)F2 intercross are present. Parental strain A/J exhibits greater age-related retinal degeneration compared to C57BL/6J. F2 animals were maintained in a dimly-lit environment and sacrificed at 8 months of age. The retinal outer nuclear layer was recorded for each animal. Eighty-six polymorphic markers at an average spacing of 13.1 cM were used for the genome scan. Previously identified QTLs Arrd1 (chr6), Arrd2 (chr10), and Arrd3 (chr16) were not detected in this cross. However, SNP analysis was used to identify positional candidate genes for Arrd1 at 35 cM. Prokr1, Gkn1, Gata2 (38.5 cM) , 2010301N04Rik, and E230015B07Rik map to the Arrd1 interval and are expressed in the eye. Antxr, Ruvbl1, and Eefsec map to the Arrd1 locus but do not exhibit co-expression with retina- or RPE-specific genes. Significant linkage to age-related retinal degeneration was detected on the X chromosome between DXMit192 (16 cM) and DXMit19 (43.2 cM). This locus is named Arrd4 (age-related retinal degeneration 4). Males hemizygous for C57BL/6J-derived alleles at Arrd4 exhibit decreased retinal degeneration compared to females with A/J-derived alleles. Thus, Arrd4 appears to have a sex-dependent effect. Suggestive linkage to age-related retinal degeneration mapped to proximal mouse Chromosome 14 between D14Mit98 (3 cM) and D14Mit60 (15 cM) with LOD=2.15. This region overlaps with a suggestive locus detected in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross. C57BL/6J-derived alleles confer susceptibility retinal degeneration in both crosses. Suggestive linkage was detected at 13 cM- 29 cM on mouse Chromosome 12 between D12Mit59 and D12Mit91 (LOD=2.24). This locus was also suggestive in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross between D12Mit60 (16 cM) and D12Mit236 (22 cM). C57BL/6J-derived alleles confer susceptibility to retinal degeneration in both crosses. A distal locus also shows suggestive linkage to retinal degeneration in (A/J x C57BL/6J)F2 animals at 53 cM - 59 cM (LOD=2.91). C57BL/6J-derived alleles at this locus confers susceptibility to retinal degeneration. Suggestive linkage unique to the (A/J x C57BL/6J)F2 cross mapped to 35 cM (D13Mit13) - 40 cM (D13Mit256) on mouse Chromosome 13 (LOD=2.85) and 22.9 cM (D17Mit51) - 34.3 cM (D17Mit20) on mouse Chromosome 17 (LOD=2.22). C57BL/6J-derived alleles at these loci confer resistance to age-related retinal degeneration.
Ruvbl1	Chr6:88442391-88474548 (+)	J:118199	Linkage analysis was performed on 170 animals from a (A/J x C57BL/6J)F2 intercross to determine if age-related retinal degeneration QTLs previously identified in a (C57BL/6J-Tyr x BALB/cByJ)F2 intercross are present. Parental strain A/J exhibits greater age-related retinal degeneration compared to C57BL/6J. F2 animals were maintained in a dimly-lit environment and sacrificed at 8 months of age. The retinal outer nuclear layer was recorded for each animal. Eighty-six polymorphic markers at an average spacing of 13.1 cM were used for the genome scan. Previously identified QTLs Arrd1 (chr6), Arrd2 (chr10), and Arrd3 (chr16) were not detected in this cross. However, SNP analysis was used to identify positional candidate genes for Arrd1 at 35 cM. Prokr1, Gkn1, Gata2 (38.5 cM) , 2010301N04Rik, and E230015B07Rik map to the Arrd1 interval and are expressed in the eye. Antxr, Ruvbl1, and Eefsec map to the Arrd1 locus but do not exhibit co-expression with retina- or RPE-specific genes. Significant linkage to age-related retinal degeneration was detected on the X chromosome between DXMit192 (16 cM) and DXMit19 (43.2 cM). This locus is named Arrd4 (age-related retinal degeneration 4). Males hemizygous for C57BL/6J-derived alleles at Arrd4 exhibit decreased retinal degeneration compared to females with A/J-derived alleles. Thus, Arrd4 appears to have a sex-dependent effect. Suggestive linkage to age-related retinal degeneration mapped to proximal mouse Chromosome 14 between D14Mit98 (3 cM) and D14Mit60 (15 cM) with LOD=2.15. This region overlaps with a suggestive locus detected in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross. C57BL/6J-derived alleles confer susceptibility retinal degeneration in both crosses. Suggestive linkage was detected at 13 cM- 29 cM on mouse Chromosome 12 between D12Mit59 and D12Mit91 (LOD=2.24). This locus was also suggestive in the (C57BL/6J-Tyr x BALB/cByJ)F2 cross between D12Mit60 (16 cM) and D12Mit236 (22 cM). C57BL/6J-derived alleles confer susceptibility to retinal degeneration in both crosses. A distal locus also shows suggestive linkage to retinal degeneration in (A/J x C57BL/6J)F2 animals at 53 cM - 59 cM (LOD=2.91). C57BL/6J-derived alleles at this locus confers susceptibility to retinal degeneration. Suggestive linkage unique to the (A/J x C57BL/6J)F2 cross mapped to 35 cM (D13Mit13) - 40 cM (D13Mit256) on mouse Chromosome 13 (LOD=2.85) and 22.9 cM (D17Mit51) - 34.3 cM (D17Mit20) on mouse Chromosome 17 (LOD=2.22). C57BL/6J-derived alleles at these loci confer resistance to age-related retinal degeneration.