Cbx2 (chromobox 2) - Rat Genome Database

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Gene: Cbx2 (chromobox 2) Mus musculus
Analyze
Symbol: Cbx2
Name: chromobox 2
RGD ID: 1558585
MGI Page MGI
Description: Enables chromatin binding activity and methylated histone binding activity. Acts upstream of or within negative regulation of transcription by RNA polymerase II. Located in euchromatin; heterochromatin; and nucleus. Part of PcG protein complex. Is expressed in several structures, including brain; early conceptus; genitourinary system; immune system; and retina nuclear layer. Human ortholog(s) of this gene implicated in 46,XY sex reversal 5. Orthologous to human CBX2 (chromobox 2).
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: chromobox homolog 2; chromobox protein homolog 2; hromobox homolog 2; M33; M33 polycomb-like protein; MOD2; modifier 3 protein; pc; polycomb
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911118,913,845 - 118,922,101 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11118,913,788 - 118,922,096 (+)EnsemblGRCm39 Ensembl
GRCm3811119,023,019 - 119,031,275 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11119,022,962 - 119,031,270 (+)EnsemblGRCm38mm10GRCm38
MGSCv3711118,884,343 - 118,892,584 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3611118,839,119 - 118,847,360 (+)NCBIMGSCv36mm8
Celera11130,767,511 - 130,775,731 (+)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1183.33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
euchromatin  (IDA)
heterochromatin  (IBA,IDA)
nuclear speck  (IEA)
nucleoplasm  (ISO)
nucleus  (IDA,ISO)
PcG protein complex  (IDA,ISO)
PRC1 complex  (IBA,ISO,ISS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. PRC1 complex diversity: where is it taking us? Gil J and O'Loghlen A, Trends Cell Biol. 2014 Jul 22. pii: S0962-8924(14)00102-0. doi: 10.1016/j.tcb.2014.06.005.
2. Male-to-female sex reversal in M33 mutant mice. Katoh-Fukui Y, etal., Nature. 1998 Jun 18;393(6686):688-92.
3. MGDs mouse GO annotations MGD data from the GO Consortium
4. MGD IEA MGD IEA
5. CBX2 gene analysis in patients with 46,XY and 46,XX gonadal disorders of sex development. Norling A, etal., Fertil Steril. 2013 Mar 1;99(3):819-826.e3. doi: 10.1016/j.fertnstert.2012.11.016. Epub 2012 Dec 7.
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. Clinical relevance of breast cancer-related genes as potential biomarkers for oral squamous cell carcinoma. Parris TZ, etal., BMC Cancer. 2014 May 7;14:324. doi: 10.1186/1471-2407-14-324.
8. Mouse MP Annotation Import Pipeline RGD automated import pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Simon JA and Kingston RE, Mol Cell. 2013 Mar 7;49(5):808-24. doi: 10.1016/j.molcel.2013.02.013.
12. Comprehensive Molecular Analyses of a Macrophage-Related Gene Signature With Regard to Prognosis, Immune Features, and Biomarkers for Immunotherapy in Hepatocellular Carcinoma Based on WGCNA and the LASSO Algorithm. Wang T, etal., Front Immunol. 2022 May 27;13:843408. doi: 10.3389/fimmu.2022.843408. eCollection 2022.
Additional References at PubMed
PMID:1352241   PMID:7555711   PMID:7782071   PMID:8672134   PMID:8889548   PMID:9043087   PMID:9312051   PMID:9367786   PMID:9571155   PMID:9716520   PMID:10349636   PMID:10369680  
PMID:10926763   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11242053   PMID:11738999   PMID:11855817   PMID:11950896   PMID:12167701   PMID:12466851   PMID:12477932   PMID:12589020  
PMID:14973489   PMID:15211353   PMID:15226823   PMID:15377996   PMID:15489334   PMID:15589172   PMID:15618518   PMID:15741318   PMID:15899914   PMID:15964995   PMID:16141072   PMID:16141073  
PMID:16537902   PMID:16687444   PMID:16786585   PMID:17001316   PMID:17043400   PMID:17296600   PMID:17726103   PMID:18311137   PMID:18927235   PMID:19833123   PMID:20059953   PMID:20412781  
PMID:20493168   PMID:20808772   PMID:20962046   PMID:21402785   PMID:21606357   PMID:21677750   PMID:21873635   PMID:22012622   PMID:22186409   PMID:23095882   PMID:23102581   PMID:23629965  
PMID:23987514   PMID:24091011   PMID:24194600   PMID:25232004   PMID:25801166   PMID:27626380   PMID:28280206   PMID:30186101   PMID:30357595   PMID:30389610   PMID:30514760   PMID:31116734  
PMID:31171700   PMID:32870972   PMID:33313949   PMID:33554859   PMID:34033867   PMID:34321999   PMID:35084365   PMID:35263754   PMID:35385744   PMID:37158107   PMID:37253089   PMID:37422020  
PMID:37553262   PMID:38355793  


Genomics

Comparative Map Data
Cbx2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911118,913,845 - 118,922,101 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11118,913,788 - 118,922,096 (+)EnsemblGRCm39 Ensembl
GRCm3811119,023,019 - 119,031,275 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11119,022,962 - 119,031,270 (+)EnsemblGRCm38mm10GRCm38
MGSCv3711118,884,343 - 118,892,584 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3611118,839,119 - 118,847,360 (+)NCBIMGSCv36mm8
Celera11130,767,511 - 130,775,731 (+)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1183.33NCBI
CBX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381779,777,311 - 79,787,983 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1779,778,148 - 79,787,983 (+)EnsemblGRCh38hg38GRCh38
GRCh371777,751,947 - 77,761,782 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361775,366,588 - 75,375,974 (+)NCBINCBI36Build 36hg18NCBI36
Celera1774,346,955 - 74,386,998 (+)NCBICelera
Cytogenetic Map17q25.3NCBI
HuRef1773,192,850 - 73,202,322 (+)NCBIHuRef
CHM1_11777,838,205 - 77,847,668 (+)NCBICHM1_1
T2T-CHM13v2.01780,675,116 - 80,685,808 (+)NCBIT2T-CHM13v2.0
Cbx2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr810104,777,054 - 104,785,922 (+)NCBIGRCr8
mRatBN7.210104,278,517 - 104,287,384 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10104,278,549 - 104,287,383 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx10109,381,786 - 109,390,623 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.010108,844,811 - 108,853,642 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.010104,199,191 - 104,208,022 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.010108,132,105 - 108,140,935 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10108,132,105 - 108,140,935 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010107,745,908 - 107,754,738 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera10102,826,793 - 102,835,641 (+)NCBICelera
Cytogenetic Map10q32.3NCBI
Cbx2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555063,046,607 - 3,053,001 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555063,045,395 - 3,053,003 (-)NCBIChiLan1.0ChiLan1.0
CBX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21995,832,646 - 95,842,081 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan117100,661,634 - 100,671,068 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01773,858,381 - 73,867,811 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11779,395,344 - 79,404,545 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1779,394,550 - 79,404,545 (+)Ensemblpanpan1.1panPan2
CBX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.191,847,867 - 1,855,923 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl91,850,874 - 1,856,328 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha92,493,222 - 2,499,752 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.092,485,745 - 2,492,274 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl92,486,079 - 2,492,265 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.192,508,944 - 2,515,470 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.092,634,412 - 2,640,931 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.092,715,682 - 2,722,211 (-)NCBIUU_Cfam_GSD_1.0
Cbx2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056022,509,894 - 2,542,662 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365943,893,772 - 3,900,000 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365943,886,926 - 3,902,459 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CBX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl122,570,851 - 2,580,337 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1122,570,841 - 2,580,336 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2122,639,429 - 2,648,428 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CBX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11671,741,476 - 71,749,234 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1671,741,500 - 71,751,817 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607743,038,495 - 43,046,487 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cbx2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248018,951,723 - 8,958,352 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248018,951,659 - 8,961,280 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cbx2
254 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1094
Count of miRNA genes:573
Interacting mature miRNAs:699
Transcripts:ENSMUST00000026662, ENSMUST00000139746
Prediction methods:Miranda, Rnahybrid, 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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
11251723Ewc5_methanol withdrawal and consumption 5 (mouse)1189869251121973369Mouse
1302034Pkccl_mprotein kinase C content in lungs (mouse)Not determined1191604608121973369Mouse
1300944Alcp20_malcohol preference locus 20 (mouse)Not determined1195403965121973369Mouse
15014785Mvlq1_mmacrovesicular liver lesion QTL 1 (mouse)1186608320120608320Mouse
1301012Vispl_mvisual placing (mouse)Not determined11101022590121973369Mouse
15039374Adip29_madiposity 29 (mouse)1186608320120608320Mouse
1301983Berr2_mberghei resistance locus 2 (mouse)Not determined1198352609121973369Mouse
1300962Cd8mts4_mCD8 memory T cell subset 4 (mouse)Not determined1196137674121973369Mouse
10043976Obq33_mobesity QTL 33 (mouse)Not determined1198500469121973369Mouse
1301057Nidd4_mnon-insulin-dependent diabetes mellitus 4 (mouse)Not determined1196810136121973369Mouse
1301095El6_mepilepsy 6 (mouse)Not determined1193229183121973369Mouse
11341721Rvfs2_mRift Valley fever susceptibility 2 (mouse)11100254186120887165Mouse
1301958Alcp18_malcohol preference locus 18 (mouse)Not determined1195403965121973369Mouse
15039376Bw42_mbody weight QTL 42 (mouse)1186608320120608320Mouse
1558753Ath19_matherosclerosis 19 (mouse)Not determined1191604608121973369Mouse
10044001Alcw8_malcohol withdrawal 8 (mouse)Not determined1199254187121973369Mouse
14747003Mancz9_mmandible centroid size 9 (mouse)1185844911119844911Mouse
27226789Feml16_mfemur length 16, 10 week (mouse)1187490826121873369Mouse
11553867Stmm5_mskin tumor modifier of MSM 5 (mouse)11100058103121973369Mouse
10044007Hbnr14_mHeligmosomoides bakeri nematode resistance 14 (mouse)Not determined1187502600121502698Mouse


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000026662   ⟹   ENSMUSP00000026662
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl11118,913,788 - 118,922,096 (+)Ensembl
GRCm38.p6 Ensembl11119,022,962 - 119,031,270 (+)Ensembl
Ensembl Acc Id: ENSMUST00000139746
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl11118,914,551 - 118,918,864 (+)Ensembl
GRCm38.p6 Ensembl11119,023,725 - 119,028,038 (+)Ensembl
RefSeq Acc Id: NM_007623   ⟹   NP_031649
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3911118,913,847 - 118,922,101 (+)NCBI
GRCm3811119,023,021 - 119,031,275 (+)NCBI
MGSCv3711118,884,343 - 118,892,584 (+)RGD
Celera11130,767,511 - 130,775,731 (+)RGD
cM Map11 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006532103   ⟹   XP_006532166
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3911118,915,073 - 118,922,100 (+)NCBI
GRCm3811119,024,247 - 119,031,274 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006532104   ⟹   XP_006532167
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3911118,913,845 - 118,922,100 (+)NCBI
GRCm3811119,023,019 - 119,031,274 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006532105   ⟹   XP_006532168
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3911118,915,073 - 118,922,100 (+)NCBI
GRCm3811119,024,247 - 119,031,274 (+)NCBI
Sequence:
RefSeq Acc Id: NP_031649   ⟸   NM_007623
- UniProtKB: O35731 (UniProtKB/Swiss-Prot),   A2ABG2 (UniProtKB/Swiss-Prot),   Q8CIA0 (UniProtKB/Swiss-Prot),   P30658 (UniProtKB/Swiss-Prot),   Q3TZG6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006532167   ⟸   XM_006532104
- Peptide Label: isoform X2
- UniProtKB: Q3TZG6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006532166   ⟸   XM_006532103
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006532168   ⟸   XM_006532105
- Peptide Label: isoform X3
- Sequence:
Ensembl Acc Id: ENSMUSP00000026662   ⟸   ENSMUST00000026662
Protein Domains
Chromo

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P30658-F1-model_v2 AlphaFold P30658 1-519 view protein structure

Promoters
RGD ID:6820542
Promoter ID:MM_KWN:10808
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney,   Liver
Transcripts:OTTMUST00000008845
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3611118,883,956 - 118,884,462 (+)MPROMDB
RGD ID:6820540
Promoter ID:MM_KWN:10809
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day3,   Brain
Transcripts:OTTMUST00000008839
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3611118,884,179 - 118,884,679 (+)MPROMDB
RGD ID:8677582
Promoter ID:EPDNEW_M16822
Type:initiation region
Name:Cbx2_1
Description:Mus musculus chromobox 2 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3811119,023,056 - 119,023,116EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:88289 AgrOrtholog
Ensembl Genes ENSMUSG00000025577 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000026662 ENTREZGENE
  ENSMUST00000026662.8 UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.50.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CBX2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CBX7_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromo-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromo/chromo_shadow_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromo_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromodomain_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:12416 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:88289 ENTREZGENE
NCBI Gene 12416 ENTREZGENE
PANTHER CHROMOBOX PROTEIN HOMOLOG 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR46860 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CBX7_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromo UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cbx2 PhenoGen
PROSITE CHROMO_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CHROMO_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CHROMO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54160 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A2ABG2 ENTREZGENE
  CBX2_MOUSE UniProtKB/Swiss-Prot
  O35731 ENTREZGENE
  P30658 ENTREZGENE
  Q3TZG6 ENTREZGENE, UniProtKB/TrEMBL
  Q3URA3_MOUSE UniProtKB/TrEMBL
  Q8CIA0 ENTREZGENE
UniProt Secondary A2ABG2 UniProtKB/Swiss-Prot
  O35731 UniProtKB/Swiss-Prot
  Q8CIA0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-07-10 Cbx2  chromobox 2  Cbx2  chromobox homolog 2 (Drosophila Pc class)  Symbol and/or name change 5135510 APPROVED