early conceptus |
embryo ectoderm |
embryo endoderm |
embryo mesoderm |
embryo mesenchyme |
extraembryonic component |
alimentary system |
auditory system |
branchial arches |
cardiovascular system |
connective tissue |
endocrine system |
exocrine system |
hemolymphoid system |
integumental system |
limbs |
liver and biliary system |
musculoskeletal system |
nervous system |
olfactory system |
reproductive system |
respiratory system |
urinary system |
visual system |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Transcription Start Site | Location | Distance from Gene 5'-end |
| Tssr35007 | Chr3:106697491-106697502 (-) | -32 bp |
| Tssr35006 | Chr3:106697459-106697470 (-) | 0 bp |
| Tssr35005 | Chr3:106697445-106697456 (-) | 14 bp |
| Tssr35004 | Chr3:106697389-106697400 (-) | 70 bp |
| Tssr35003 | Chr3:106697363-106697388 (-) | 89 bp |
| Tssr35002 | Chr3:106697350-106697361 (-) | 109 bp |
| Tssr35001 | Chr3:106697319-106697344 (-) | 133 bp |
| Tssr35000 | Chr3:106695884-106695895 (-) | 1,575 bp |
| Tssr34999 | Chr3:106695394-106695434 (-) | 2,051 bp |
| Tssr1002 | Chr3:106695328-106695343 (-) | 2,129 bp |
| Tssr1001 | Chr3:106683193-106683216 (-) | 14,260 bp |
| Tssr34998 | Chr3:106675271-106675321 (-) | 22,169 bp |
| Tssr34997 | Chr3:106674678-106674733 (-) | 22,759 bp |
| Tssr34996 | Chr3:106674097-106674127 (-) | 23,353 bp |
| Tssr34995 | Chr3:106674042-106674059 (-) | 23,414 bp |
| Tssr34994 | Chr3:106673987-106674008 (-) | 23,467 bp |
| Tssr34993 | Chr3:106673794-106673817 (-) | 23,659 bp |
| Tssr34992 | Chr3:106673741-106673781 (-) | 23,704 bp |
| Tssr34991 | Chr3:106670554-106670603 (-) | 26,886 bp |
| Tssr34990 | Chr3:106669433-106669497 (-) | 28,000 bp |
| Tssr34989 | Chr3:106668117-106668128 (-) | 29,342 bp |
| Tssr34988 | Chr3:106667912-106667918 (-) | 29,550 bp |
| Tssr34987 | Chr3:106667832-106667846 (-) | 29,626 bp |
| Tssr34986 | Chr3:106667785-106667801 (-) | 29,672 bp |
| QTL | Genetic Location* | Genome Location (GRCm39) | Reference | QTL Note |
| Cia5 | Chr3, 37.01 cM | Chr3:83046658-83046795 | J:101473 | Microarray gene chip technology was used to identify differentially expressed candidate genes for the arthritis QTL on mouse Chromosome 3 named Cia5. The Cia5 QTL microarray chip contains 163 genes found between 95.3 Mb and 109.7 Mb on mouse Chromosome 3. (This region spans markers D3Mit101 to D3Mit103.) Gene expression in lymph nodes, spleen, and paws was compared between the resistant Cia5 congenic and susceptible B10.RIII background strain. Animals were immunized with 100 ug of bovine CII at 12 weeks of age. Gene expression was evaluated at 0, 6, and 12 days after immunization. A total of 26 genes in the Cia5 locus were found to have significant expression differences (P<0.05) between the congenic and B10.RIII. These genes were found in 2 clusters corresponding to Cia21 and Cia22. Some notable candidate genes are described below. Chi3l3 (50.5 cM; 105.9 Mb) is downregulated in congenic animals in spleen (all time points) and lymph nodes (day 6). Vav3 (109.1 Mb) is upregulated in congenic animals in spleen (all time points), lymph nodes (day 0), and paws (days 6 and 12). Gpr89 (96.3 Mb) is upregulated in congenic animals in spleen (all time points) and lymph nodes (day 0). Ptpn22 (103.2 Mb) is downregulated in congenic animals in lymph nodes (day 0). Cd53 (50.5 cM; 106.5 Mb) is upregulated in B10.RIII in spleen (day 12) and lymph nodes (day 0). Gstm1 (107.8 Mb) is upregulated in B10.RIII in spleen and lymph nodes at day 0, but is downregulated after immunization. |
| Cia5 | Chr3, 37.01 cM | Chr3:83046658-83046795 | J:81372 | Microarray gene expression analysis was used to identify candidate genes for QTLs associated with collagen-induced arthritis. RNA from inflamed paws of collagen-treated mice were used in the microarray analysis and compared to RNA from normal paws. 223 genes showed a four-fold or greater expression difference between inflamed and normal paws. Nine of these genes are located near previously identified arthritis severity/susceptibility QTLs and may be considered for candidates. For Cia1 on mouse Chromosome 17 (18.6 cM near the H2 locus) differential expression was observed for H2-Eb1 (18.66 cM) and H2-T23 (19.73 cM). For Cia2 and Cia4 on mouse Chromosome 2 (both are located at 34 cM) differential expression was observed for Fap (36 cM) and Gcg (36 cM). For Cia3 (48.7 cM) and Cia6 (30 cM) on mouse Chromosome 6 differential expression was observed for Raf1 (52.5 cM) and Slc6a6 (38.2 cM), respectively. For Cia5 (40 cM) on mouse Chromosome 4 differential expression was observed for Ctsk (47.9 cM) and Cd53(50.5 cM). For Cia8 (40.4 cM) on mouse Chromosome 10 differential expression was observed for Bsg (42.4 cM). |
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO) |
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last database update 11/12/2024 MGI 6.24 |
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