Cbx3 (chromobox 3) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Cbx3 (chromobox 3) Rattus norvegicus
Analyze
Symbol: Cbx3
Name: chromobox 3
RGD ID: 1549705
Description: Predicted to enable several functions, including histone methyltransferase binding activity; identical protein binding activity; and transcription coregulator binding activity. Involved in cellular response to dexamethasone stimulus. Part of senescence-associated heterochromatin focus. Orthologous to human CBX3 (chromobox 3); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: chromobox homolog 3; chromobox homolog 3 (HP1 gamma homolog, Drosophila); chromobox protein homolog 3; heterochromatin protein 1 gamma; HP1 gamma; Hp1-gamma; MGC105792; MGC105793; MGC156678; MGC94711
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Cbx3l3  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8481,876,155 - 81,889,912 (+)NCBIGRCr8
mRatBN7.2480,545,450 - 80,559,284 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl480,546,010 - 80,559,283 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx485,770,325 - 85,783,553 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0481,545,719 - 81,558,947 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0479,985,145 - 79,998,366 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0481,243,809 - 81,257,898 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl481,244,469 - 81,257,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04145,909,973 - 145,924,082 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4479,707,325 - 79,720,100 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera475,446,761 - 75,459,968 (+)NCBICelera
Cytogenetic Map4q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
4,4'-sulfonyldiphenol  (EXP,ISO)
9-cis-retinoic acid  (ISO)
acetazolamide  (ISO)
aflatoxin B1  (ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-retinoic acid  (ISO)
aristolochic acid A  (ISO)
Aroclor 1254  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (EXP)
bortezomib  (ISO)
Brodifacoum  (EXP)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
diazinon  (ISO)
dicrotophos  (ISO)
diquat  (ISO)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethyl methanesulfonate  (ISO)
finasteride  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
FR900359  (ISO)
gentamycin  (EXP)
gold atom  (ISO)
gold(0)  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
methidathion  (ISO)
methyl methanesulfonate  (ISO)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
nicotine  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (EXP)
pinosylvin  (ISO)
pirinixic acid  (ISO)
quinoline  (ISO)
raloxifene  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
tamibarotene  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (EXP)
thimerosal  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trans-pinosylvin  (ISO)
Tributyltin oxide  (ISO)
trichloroethene  (EXP)
trimellitic anhydride  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Glucocorticoids induce long-lasting effects in neural stem cells resulting in senescence-related alterations. Bose R, etal., Cell Death Dis. 2010 Nov 4;1:e92.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
7. The heterochromatin protein 1 family is regulated in prostate development and cancer. Shapiro E, etal., J Urol. 2008 Jun;179(6):2435-9. doi: 10.1016/j.juro.2008.01.091. Epub 2008 Apr 23.
8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:8663349   PMID:9636147   PMID:10504293   PMID:10562550   PMID:11101528   PMID:11124534   PMID:15322135   PMID:15469996   PMID:16287503   PMID:16880268   PMID:17540172   PMID:19135898  
PMID:19486527   PMID:20219459   PMID:21888893   PMID:24413057   PMID:27248496   PMID:30305677   PMID:35352799  


Genomics

Comparative Map Data
Cbx3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8481,876,155 - 81,889,912 (+)NCBIGRCr8
mRatBN7.2480,545,450 - 80,559,284 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl480,546,010 - 80,559,283 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx485,770,325 - 85,783,553 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0481,545,719 - 81,558,947 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0479,985,145 - 79,998,366 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0481,243,809 - 81,257,898 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl481,244,469 - 81,257,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04145,909,973 - 145,924,082 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4479,707,325 - 79,720,100 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera475,446,761 - 75,459,968 (+)NCBICelera
Cytogenetic Map4q24NCBI
CBX3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38726,201,443 - 26,213,607 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl726,201,162 - 26,213,607 (+)EnsemblGRCh38hg38GRCh38
GRCh37726,241,063 - 26,253,227 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36726,207,624 - 26,219,501 (+)NCBINCBI36Build 36hg18NCBI36
Build 34726,014,563 - 26,026,216NCBI
Celera726,230,084 - 26,241,954 (+)NCBICelera
Cytogenetic Map7p15.2NCBI
HuRef726,122,745 - 26,135,135 (+)NCBIHuRef
CHM1_1726,234,045 - 26,252,803 (+)NCBICHM1_1
T2T-CHM13v2.0726,337,121 - 26,349,288 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2726,291,980 - 26,304,374 (+)NCBI
Cbx3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39651,447,596 - 51,460,684 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl651,447,340 - 51,460,684 (+)EnsemblGRCm39 Ensembl
GRCm38651,470,154 - 51,483,704 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl651,470,360 - 51,483,704 (+)EnsemblGRCm38mm10GRCm38
MGSCv37651,420,615 - 51,433,703 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36651,399,943 - 51,426,513 (+)NCBIMGSCv36mm8
Celera651,988,350 - 52,001,439 (+)NCBICelera
Cytogenetic Map6B3NCBI
cM Map624.89NCBI
Cbx3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541028,043,110 - 28,052,616 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541028,042,627 - 28,052,616 (+)NCBIChiLan1.0ChiLan1.0
CBX3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2631,031,316 - 31,043,199 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1779,356,042 - 79,367,925 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0726,847,247 - 26,859,339 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1726,450,411 - 26,462,563 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl726,450,411 - 26,462,350 (+)Ensemblpanpan1.1panPan2
CBX3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11439,510,694 - 39,520,796 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1439,510,112 - 39,519,809 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1438,999,924 - 39,011,647 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01439,447,799 - 39,459,552 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1439,447,974 - 39,459,552 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11439,562,860 - 39,574,595 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01439,250,004 - 39,261,736 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01439,600,666 - 39,612,399 (+)NCBIUU_Cfam_GSD_1.0
Cbx3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511883,769,172 - 83,777,598 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364782,981,228 - 2,989,324 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364782,981,218 - 2,989,329 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CBX3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1846,193,140 - 46,204,714 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11846,193,138 - 46,205,114 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21850,968,275 - 50,980,400 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CBX3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12132,154,707 - 32,166,843 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2132,155,839 - 32,166,114 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604272,523,268 - 72,535,452 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cbx3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247394,332,975 - 4,343,155 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247394,331,948 - 4,342,353 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cbx3
33 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:696
Count of miRNA genes:294
Interacting mature miRNAs:369
Transcripts:ENSRNOT00000015828, ENSRNOT00000044407
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)470362013132642728Rat
61364Iddm2Insulin dependent diabetes mellitus QTL 2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)478885890102684881Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)462277855128289560Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in mean arterial blood pressure (CMO:0002035)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in systolic blood pressure (CMO:0000747)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in pulse pressure (CMO:0001882)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)462933508114921294Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
70167Bw22Body weight QTL 223.1body mass (VT:0001259)body weight (CMO:0000012)476647384117676292Rat
724522Bp146Blood pressure QTL 1462.20.0021arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)473630210118630210Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
631556Bp135Blood pressure QTL 1350.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)478881294117676292Rat
631646Stl4Serum triglyceride level QTL 46.50.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)473169846132642728Rat
631651Bp124Blood pressure QTL 1243arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462879517107879517Rat
631662Hcar2Hepatocarcinoma resistance QTL 23.10.0003liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)478878504123878504Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711443291360801Rat
634311Sach7Saccharin preference QTL 7taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)45711443281266970Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)470808386115808386Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)470808386115808386Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
1358363Sradr3Stress Responsive Adrenal Weight QTL 36.19adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)457486946102486946Rat
1357342Bw40Body weight QTL 400.001body mass (VT:0001259)body weight (CMO:0000012)476647384117676292Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)45843213392991462Rat
1549839Bw52Body weight QTL 520.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658115089733Rat
1549843Bw53Body weight QTL 530.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658103194791Rat
1578657Bss12Bone structure and strength QTL 128.9femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)460220938105220938Rat
1578658Bss13Bone structure and strength QTL 138femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)460220938105220938Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)456698790126192555Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302051Pia28Pristane induced arthritis QTL 285.30.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)473630210118630210Rat
2300179Bmd50Bone mineral density QTL 505.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)460928534105928534Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
2312569Pur19Proteinuria QTL 193.40.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)46588210796130297Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2317586Eae25Experimental allergic encephalomyelitis QTL 259.300000190734863nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)47888281783007655Rat
2317586Eae25Experimental allergic encephalomyelitis QTL 259.300000190734863nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)47888281783007655Rat
2317586Eae25Experimental allergic encephalomyelitis QTL 259.300000190734863nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)47888281783007655Rat
2317586Eae25Experimental allergic encephalomyelitis QTL 259.300000190734863nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)47888281783007655Rat
6478743Anxrr40Anxiety related response QTL 400.83076defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478772Anxrr49Anxiety related response QTL 490.15488defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
6478684Anxrr30Anxiety related response QTL 300.00087defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
7394826Bw126Body weight QTL 1260.002body mass (VT:0001259)body weight gain (CMO:0000420)46293326987483707Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552807Vie4Viral induced encephalitis QTL 47.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)46293350882490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat

Markers in Region
UniSTS:238126  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21629,187,987 - 29,188,532 (+)MAPPERmRatBN7.2
mRatBN7.2568,280,773 - 68,281,315 (+)MAPPERmRatBN7.2
Rnor_6.0570,462,975 - 70,463,516NCBIRnor6.0
Rnor_6.01632,509,512 - 32,510,056NCBIRnor6.0
Rnor_5.01632,344,352 - 32,344,896UniSTSRnor5.0
Rnor_5.0574,620,539 - 74,621,080UniSTSRnor5.0
RGSC_v3.4571,095,184 - 71,095,725UniSTSRGSC3.4
RGSC_v3.41632,507,686 - 32,508,230UniSTSRGSC3.4
Celera1629,182,635 - 29,183,179UniSTS
Celera567,175,084 - 67,175,625UniSTS
Cytogenetic Map5q24UniSTS
Cytogenetic Map16p12UniSTS
Cytogenetic Map4q24UniSTS
RH137086  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map4q24UniSTS
RH139245  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23118,679,429 - 118,679,551 (+)MAPPERmRatBN7.2
mRatBN7.2480,545,055 - 80,545,177 (+)MAPPERmRatBN7.2
Rnor_6.0481,243,498 - 81,243,619NCBIRnor6.0
Rnor_6.03124,014,086 - 124,014,207NCBIRnor6.0
Rnor_5.04145,909,682 - 145,909,803UniSTSRnor5.0
Rnor_5.03130,510,840 - 130,510,961UniSTSRnor5.0
RGSC_v3.43119,167,545 - 119,167,666UniSTSRGSC3.4
RGSC_v3.4479,706,329 - 79,706,450UniSTSRGSC3.4
Celera475,445,776 - 75,445,897UniSTS
Celera3117,485,561 - 117,485,682UniSTS
RH 3.4 Map4526.02UniSTS
Cytogenetic Map4q24UniSTS
Cytogenetic Map3q36UniSTS
AW528373  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2480,546,621 - 80,546,806 (+)MAPPERmRatBN7.2
Rnor_6.0481,245,069 - 81,245,253NCBIRnor6.0
Rnor_5.04145,911,253 - 145,911,437UniSTSRnor5.0
RGSC_v3.4479,707,896 - 79,708,080UniSTSRGSC3.4
Celera475,447,332 - 75,447,516UniSTS
RH 3.4 Map4489.81UniSTS
Cytogenetic Map4q24UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 54 38 19 38 8 11 74 35 41 11 8
Low 3 3 3
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000015828   ⟹   ENSRNOP00000015828
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl480,546,010 - 80,559,281 (+)Ensembl
Rnor_6.0 Ensembl481,244,498 - 81,257,897 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000044407   ⟹   ENSRNOP00000046151
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl480,546,022 - 80,559,283 (+)Ensembl
Rnor_6.0 Ensembl481,244,469 - 81,257,897 (+)Ensembl
RefSeq Acc Id: NM_001008313   ⟹   NP_001008314
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8481,876,679 - 81,889,912 (+)NCBI
mRatBN7.2480,546,051 - 80,559,284 (+)NCBI
Rnor_6.0481,244,498 - 81,257,898 (+)NCBI
Rnor_5.04145,909,973 - 145,924,082 (+)NCBI
RGSC_v3.4479,707,325 - 79,720,100 (+)RGD
Celera475,446,761 - 75,459,968 (+)RGD
Sequence:
RefSeq Acc Id: XM_006236484   ⟹   XP_006236546
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8481,876,585 - 81,889,912 (+)NCBI
mRatBN7.2480,545,450 - 80,559,284 (+)NCBI
Rnor_6.0481,243,809 - 81,257,898 (+)NCBI
Rnor_5.04145,909,973 - 145,924,082 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039107302   ⟹   XP_038963230
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8481,877,389 - 81,889,912 (+)NCBI
mRatBN7.2480,546,562 - 80,559,284 (+)NCBI
RefSeq Acc Id: XM_039107304   ⟹   XP_038963232
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8481,877,116 - 81,889,912 (+)NCBI
mRatBN7.2480,546,488 - 80,559,284 (+)NCBI
RefSeq Acc Id: XM_039107305   ⟹   XP_038963233
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8481,876,155 - 81,889,912 (+)NCBI
mRatBN7.2480,545,450 - 80,559,284 (+)NCBI
RefSeq Acc Id: XM_039107306   ⟹   XP_038963234
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8481,876,582 - 81,889,912 (+)NCBI
mRatBN7.2480,545,450 - 80,559,284 (+)NCBI
RefSeq Acc Id: XM_063285770   ⟹   XP_063141840
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8481,876,395 - 81,889,912 (+)NCBI
RefSeq Acc Id: NP_001008314   ⟸   NM_001008313
- UniProtKB: Q5RJK5 (UniProtKB/TrEMBL),   A0JPM8 (UniProtKB/TrEMBL),   D3ZRS6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006236546   ⟸   XM_006236484
- Peptide Label: isoform X1
- UniProtKB: Q5RJK5 (UniProtKB/TrEMBL),   A0JPM8 (UniProtKB/TrEMBL),   D3ZRS6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000046151   ⟸   ENSRNOT00000044407
RefSeq Acc Id: ENSRNOP00000015828   ⟸   ENSRNOT00000015828
RefSeq Acc Id: XP_038963234   ⟸   XM_039107306
- Peptide Label: isoform X2
- UniProtKB: D3ZRS6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038963233   ⟸   XM_039107305
- Peptide Label: isoform X1
- UniProtKB: Q5RJK5 (UniProtKB/TrEMBL),   A0JPM8 (UniProtKB/TrEMBL),   D3ZRS6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038963232   ⟸   XM_039107304
- Peptide Label: isoform X1
- UniProtKB: Q5RJK5 (UniProtKB/TrEMBL),   A0JPM8 (UniProtKB/TrEMBL),   D3ZRS6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038963230   ⟸   XM_039107302
- Peptide Label: isoform X1
- UniProtKB: Q5RJK5 (UniProtKB/TrEMBL),   A0JPM8 (UniProtKB/TrEMBL),   D3ZRS6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063141840   ⟸   XM_063285770
- Peptide Label: isoform X2
Protein Domains
Chromo

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5RJK5-F1-model_v2 AlphaFold Q5RJK5 1-183 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13693051
Promoter ID:EPDNEW_R3571
Type:initiation region
Name:Cbx3_1
Description:chromobox 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0481,244,470 - 81,244,530EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1549705 AgrOrtholog
BioCyc Gene G2FUF-44855 BioCyc
Ensembl Genes ENSRNOG00000011814 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000030902 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015828 ENTREZGENE
  ENSRNOT00000015828.8 UniProtKB/TrEMBL
  ENSRNOT00000044407.5 UniProtKB/TrEMBL
  ENSRNOT00000066349.3 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.40 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7313954 IMAGE-MGC_LOAD
  IMAGE:7380822 IMAGE-MGC_LOAD
InterPro CBX3 UniProtKB/TrEMBL
  Chromo_dom_subgr UniProtKB/TrEMBL
  Chromo_domain UniProtKB/TrEMBL
  Chromo_shadow_dom UniProtKB/TrEMBL
  Chromodomain UniProtKB/TrEMBL
  Chromodomain-like UniProtKB/TrEMBL
  Chromodomain_CS UniProtKB/TrEMBL
KEGG Report rno:297093 UniProtKB/TrEMBL
MGC_CLONE MGC:105793 IMAGE-MGC_LOAD
  MGC:156678 IMAGE-MGC_LOAD
NCBI Gene 297093 ENTREZGENE
PANTHER CHROMATOR, ISOFORM A-RELATED UniProtKB/TrEMBL
  CHROMOBOX PROTEIN UniProtKB/TrEMBL
  CHROMOBOX PROTEIN HOMOLOG 3 UniProtKB/TrEMBL
Pfam Chromo UniProtKB/TrEMBL
  Chromo_shadow UniProtKB/TrEMBL
PhenoGen Cbx3 PhenoGen
PRINTS CHROMODOMAIN UniProtKB/TrEMBL
PROSITE CHROMO_1 UniProtKB/TrEMBL
  CHROMO_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011814 RatGTEx
  ENSRNOG00000030902 RatGTEx
SMART CHROMO UniProtKB/TrEMBL
  ChSh UniProtKB/TrEMBL
Superfamily-SCOP Chromodomain-like UniProtKB/TrEMBL
UniProt A0JPM8 ENTREZGENE, UniProtKB/TrEMBL
  D3ZRS6 ENTREZGENE, UniProtKB/TrEMBL
  Q5RJK5 ENTREZGENE, UniProtKB/TrEMBL
  Q5RJL1_RAT UniProtKB/TrEMBL
UniProt Secondary F7EWT2 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-02 Cbx3  chromobox 3  Cbx3  chromobox homolog 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-07-29 Cbx3  chromobox homolog 3  Cbx3  chromobox homolog 3 (HP1 gamma homolog, Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-09-15 Cbx3  chromobox homolog 3 (HP1 gamma homolog, Drosophila)      Symbol and Name status set to provisional 70820 PROVISIONAL