CBX4 (chromobox 4) - Rat Genome Database

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Pathways
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Gene: CBX4 (chromobox 4) Homo sapiens
Analyze
Symbol: CBX4
Name: chromobox 4
RGD ID: 1348844
HGNC Page HGNC:1554
Description: Enables SUMO binding activity; SUMO ligase activity; and enzyme binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nuclear body. Part of PRC1 complex. Implicated in hepatocellular carcinoma. Biomarker of hepatocellular carcinoma.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: chromobox homolog 4 (Pc class homolog, Drosophila); chromobox protein homolog 4; chromobox-like protein 4; E3 SUMO-protein ligase CBX4; hPC2; NBP16; NS5ATP1-binding protein 16; Pc class 2 homolog; PC2; polycomb 2 homolog
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381779,833,156 - 79,839,440 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1779,833,156 - 79,839,440 (-)EnsemblGRCh38hg38GRCh38
GRCh371777,806,955 - 77,813,239 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361775,421,550 - 75,427,808 (-)NCBINCBI36Build 36hg18NCBI36
Build 341775,421,550 - 75,427,808NCBI
Celera1774,433,438 - 74,439,695 (-)NCBICelera
Cytogenetic Map17q25.3NCBI
HuRef1773,247,786 - 73,258,221 (-)NCBIHuRef
CHM1_11777,893,186 - 77,899,450 (-)NCBICHM1_1
T2T-CHM13v2.01780,730,965 - 80,737,249 (-)NCBIT2T-CHM13v2.0
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
(-)-epigallocatechin 3-gallate  (EXP)
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (ISO)
antimycin A  (EXP)
aristolochic acid A  (EXP)
arsane  (EXP)
arsenic atom  (EXP)
arsenite(3-)  (EXP)
arsenous acid  (EXP)
atrazine  (EXP)
benzo[a]pyrene  (EXP)
benzo[a]pyrene diol epoxide I  (EXP)
bisphenol A  (EXP,ISO)
butan-1-ol  (EXP)
caffeine  (EXP)
carbon nanotube  (ISO)
chloropicrin  (EXP)
cisplatin  (EXP)
cobalt dichloride  (EXP)
copper(II) sulfate  (EXP)
coumestrol  (EXP)
cyclosporin A  (EXP)
deguelin  (EXP)
depsipeptide  (EXP)
diarsenic trioxide  (EXP)
diethyl maleate  (EXP)
doxorubicin  (EXP)
endosulfan  (ISO)
enzyme inhibitor  (EXP)
epoxiconazole  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (EXP)
fenpyroximate  (EXP)
folic acid  (ISO)
formaldehyde  (EXP)
FR900359  (EXP)
leflunomide  (EXP)
Licochalcone B  (EXP)
lipopolysaccharide  (EXP)
methyl methanesulfonate  (EXP)
methylisothiazolinone  (EXP)
methylmercury chloride  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
niclosamide  (EXP)
orphenadrine  (ISO)
ozone  (EXP)
p-menthan-3-ol  (EXP)
paracetamol  (EXP,ISO)
perfluorononanoic acid  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
picoxystrobin  (EXP)
pirinixic acid  (ISO)
potassium chromate  (EXP)
pregnenolone 16alpha-carbonitrile  (ISO)
silicon dioxide  (EXP,ISO)
sodium arsenite  (ISO)
sunitinib  (EXP)
tebufenpyrad  (EXP)
tetrachloromethane  (ISO)
thifluzamide  (EXP)
thioacetamide  (ISO)
trichloroethene  (ISO)
tungsten  (ISO)
tunicamycin  (EXP)
urethane  (EXP)
valproic acid  (EXP,ISO)
vinclozolin  (ISO)
XL147  (ISO)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nuclear body  (IDA,IEA)
nuclear speck  (IEA)
nucleoplasm  (IDA,TAS)
nucleus  (IDA,IEA,TAS)
PcG protein complex  (IDA,IEA)
PRC1 complex  (IBA,IDA,IEA)

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. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
3. Polycomb chromobox 4 enhances migration and pulmonary metastasis of hepatocellular carcinoma cell line MHCC97L. Mei Z, etal., Sci China Life Sci. 2014 Jun;57(6):610-7. doi: 10.1007/s11427-014-4663-9. Epub 2014 May 16.
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. 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.
7. Chromobox homolog 4 is correlated with prognosis and tumor cell growth in hepatocellular carcinoma. Wang B, etal., Ann Surg Oncol. 2013 Dec;20 Suppl 3:S684-92. doi: 10.1245/s10434-013-3171-7. Epub 2013 Aug 14.
Additional References at PubMed
PMID:9199346   PMID:9315667   PMID:9367786   PMID:9858531   PMID:9858600   PMID:11583618   PMID:12101246   PMID:12167701   PMID:12477932   PMID:12679040   PMID:12700765   PMID:12829790  
PMID:14638676   PMID:15231748   PMID:15489334   PMID:15563468   PMID:15592428   PMID:15710417   PMID:16009940   PMID:16061479   PMID:16169070   PMID:17018294   PMID:17081983   PMID:17087506  
PMID:17332741   PMID:17428788   PMID:17439403   PMID:18029348   PMID:18178578   PMID:18408014   PMID:18453536   PMID:18567530   PMID:18927235   PMID:19336002   PMID:19454010   PMID:19636380  
PMID:19933700   PMID:20098713   PMID:20176810   PMID:20351170   PMID:20361981   PMID:20601937   PMID:20850016   PMID:21145359   PMID:21256122   PMID:21282530   PMID:21288202   PMID:21549310  
PMID:21873635   PMID:21885019   PMID:22028491   PMID:22078878   PMID:22325352   PMID:22467880   PMID:22825850   PMID:22889411   PMID:22897849   PMID:23404503   PMID:23667531   PMID:23970103  
PMID:24163370   PMID:24434214   PMID:24457600   PMID:24460908   PMID:24528284   PMID:24912682   PMID:24981860   PMID:25281560   PMID:25447205   PMID:25766328   PMID:26186194   PMID:26496610  
PMID:26841866   PMID:26871637   PMID:27068747   PMID:27211601   PMID:27505670   PMID:27647897   PMID:27705803   PMID:27864346   PMID:28514442   PMID:28680062   PMID:28740167   PMID:28805822  
PMID:28839133   PMID:28842558   PMID:29180619   PMID:29229426   PMID:29507755   PMID:29509190   PMID:29539416   PMID:29940764   PMID:30317550   PMID:30419336   PMID:30554943   PMID:30804502  
PMID:30917318   PMID:31091453   PMID:31211140   PMID:31393050   PMID:31470122   PMID:31527615   PMID:31581881   PMID:31724308   PMID:31753913   PMID:32111827   PMID:32141558   PMID:32296183  
PMID:32416067   PMID:32552912   PMID:32926159   PMID:33387960   PMID:33464142   PMID:33660365   PMID:33849069   PMID:33961781   PMID:34079125   PMID:34316702   PMID:34795231   PMID:34856763  
PMID:34980138   PMID:35013218   PMID:35251476   PMID:35271311   PMID:35358396   PMID:35652658   PMID:35819589   PMID:35880565   PMID:35944360   PMID:35963709   PMID:36089195   PMID:36215729  
PMID:36373674   PMID:36574265   PMID:36688959   PMID:36793866   PMID:36931259   PMID:37071664   PMID:38360978   PMID:38538251  


Genomics

Comparative Map Data
CBX4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381779,833,156 - 79,839,440 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1779,833,156 - 79,839,440 (-)EnsemblGRCh38hg38GRCh38
GRCh371777,806,955 - 77,813,239 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361775,421,550 - 75,427,808 (-)NCBINCBI36Build 36hg18NCBI36
Build 341775,421,550 - 75,427,808NCBI
Celera1774,433,438 - 74,439,695 (-)NCBICelera
Cytogenetic Map17q25.3NCBI
HuRef1773,247,786 - 73,258,221 (-)NCBIHuRef
CHM1_11777,893,186 - 77,899,450 (-)NCBICHM1_1
T2T-CHM13v2.01780,730,965 - 80,737,249 (-)NCBIT2T-CHM13v2.0
Cbx4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911118,968,399 - 118,977,067 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11118,968,399 - 118,977,047 (-)EnsemblGRCm39 Ensembl
GRCm3811119,077,571 - 119,086,237 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11119,077,573 - 119,086,221 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711118,938,885 - 118,947,551 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3611118,896,245 - 118,902,231 (-)NCBIMGSCv36mm8
Celera11130,821,957 - 130,830,758 (-)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1183.34NCBI
Cbx4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr810104,835,685 - 104,841,727 (-)NCBIGRCr8
mRatBN7.210104,337,140 - 104,343,210 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10104,336,876 - 104,356,706 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.010108,190,947 - 108,196,455 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10108,190,995 - 108,196,217 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010107,803,761 - 107,809,306 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera10102,881,315 - 102,890,183 (-)NCBICelera
Cytogenetic Map10q32.3NCBI
Cbx4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555062,998,237 - 3,002,788 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555062,998,241 - 3,002,788 (+)NCBIChiLan1.0ChiLan1.0
CBX4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21995,887,592 - 95,893,876 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan117100,716,535 - 100,722,821 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01773,913,264 - 73,919,540 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11779,450,190 - 79,458,866 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1779,449,919 - 79,458,866 (-)Ensemblpanpan1.1panPan2
CBX4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.191,799,847 - 1,807,500 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl91,802,047 - 1,807,690 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha92,441,071 - 2,447,341 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.092,433,610 - 2,439,872 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl92,433,687 - 2,440,062 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.192,456,843 - 2,463,104 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.092,582,319 - 2,588,578 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.092,663,556 - 2,669,818 (+)NCBIUU_Cfam_GSD_1.0
Cbx4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056022,461,814 - 2,468,024 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365943,943,924 - 3,950,196 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365943,943,933 - 3,950,124 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CBX4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl122,521,027 - 2,527,241 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1122,520,913 - 2,527,245 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2122,591,117 - 2,597,525 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CBX4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11671,795,919 - 71,802,184 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1671,795,862 - 71,802,051 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607743,093,037 - 43,099,314 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cbx4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248019,003,059 - 9,008,203 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248019,002,290 - 9,008,305 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in CBX4
24 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17q25.3(chr17:78901959-83086677)x3 copy number gain See cases [RCV000050934] Chr17:78901959..83086677 [GRCh38]
Chr17:76898041..81044553 [GRCh37]
Chr17:74409636..78637842 [NCBI36]
Chr17:17q25.3		 pathogenic
GRCh38/hg38 17q25.3(chr17:78092236-83086677)x3 copy number gain See cases [RCV000050685] Chr17:78092236..83086677 [GRCh38]
Chr17:76088317..81044553 [GRCh37]
Chr17:73599912..78637842 [NCBI36]
Chr17:17q25.3		 pathogenic
GRCh38/hg38 17q24.3-25.3(chr17:69209079-83086677)x3 copy number gain See cases [RCV000052486] Chr17:69209079..83086677 [GRCh38]
Chr17:67205220..81044553 [GRCh37]
Chr17:64716815..78637842 [NCBI36]
Chr17:17q24.3-25.3		 pathogenic
GRCh38/hg38 17q25.3(chr17:78918650-83021095)x3 copy number gain See cases [RCV000052497] Chr17:78918650..83021095 [GRCh38]
Chr17:76914732..80978971 [GRCh37]
Chr17:74426327..78572260 [NCBI36]
Chr17:17q25.3		 pathogenic
GRCh38/hg38 17q23.2-25.3(chr17:36449220-83086677)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|See cases [RCV000052483] Chr17:36449220..83086677 [GRCh38]
Chr17:58617905..81044553 [GRCh37]
Chr17:55972687..78637842 [NCBI36]
Chr17:17q23.2-25.3		 pathogenic
NM_003655.2(CBX4):c.971C>T (p.Pro324Leu) single nucleotide variant Malignant melanoma [RCV000063312] Chr17:79834671 [GRCh38]
Chr17:77808470 [GRCh37]
Chr17:75423065 [NCBI36]
Chr17:17q25.3		 not provided
NM_003655.2(CBX4):c.970C>T (p.Pro324Ser) single nucleotide variant Malignant melanoma [RCV000063313] Chr17:79834672 [GRCh38]
Chr17:77808471 [GRCh37]
Chr17:75423066 [NCBI36]
Chr17:17q25.3		 not provided
GRCh38/hg38 17q25.3(chr17:78225356-80099979)x1 copy number loss See cases [RCV000135703] Chr17:78225356..80099979 [GRCh38]
Chr17:76221437..78073778 [GRCh37]
Chr17:73733032..75688373 [NCBI36]
Chr17:17q25.3		 likely pathogenic
GRCh38/hg38 17q24.3-25.3(chr17:69916435-83102552)x3 copy number gain See cases [RCV000143342] Chr17:69916435..83102552 [GRCh38]
Chr17:67912576..81048189 [GRCh37]
Chr17:65424171..78653717 [NCBI36]
Chr17:17q24.3-25.3		 pathogenic
GRCh37/hg19 17q25.1-25.3(chr17:73951701-81041938)x3 copy number gain See cases [RCV000447539] Chr17:73951701..81041938 [GRCh37]
Chr17:17q25.1-25.3		 pathogenic
GRCh37/hg19 17q24.2-25.3(chr17:64241326-81041938)x3 copy number gain See cases [RCV000447577] Chr17:64241326..81041938 [GRCh37]
Chr17:17q24.2-25.3		 pathogenic
GRCh37/hg19 17q25.3(chr17:77679924-78559726)x3 copy number gain See cases [RCV000448916] Chr17:77679924..78559726 [GRCh37]
Chr17:17q25.3		 uncertain significance
GRCh37/hg19 17q21.31-25.3(chr17:42580684-81085615)x3 copy number gain See cases [RCV000447823] Chr17:42580684..81085615 [GRCh37]
Chr17:17q21.31-25.3		 pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938) copy number gain See cases [RCV000511439] Chr17:526..81041938 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
GRCh37/hg19 17q25.1-25.3(chr17:73951701-81041938)x3 copy number gain See cases [RCV000510919] Chr17:73951701..81041938 [GRCh37]
Chr17:17q25.1-25.3		 pathogenic
GRCh37/hg19 17q24.2-25.3(chr17:67002415-81041938)x3 copy number gain See cases [RCV000512573] Chr17:67002415..81041938 [GRCh37]
Chr17:17q24.2-25.3		 pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938)x3 copy number gain See cases [RCV000512441] Chr17:526..81041938 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
GRCh37/hg19 17q24.1-25.3(chr17:63689671-81041938)x3 copy number gain not provided [RCV000683952] Chr17:63689671..81041938 [GRCh37]
Chr17:17q24.1-25.3		 pathogenic
GRCh37/hg19 17q25.3(chr17:76552611-81041938)x3 copy number gain not provided [RCV000683965] Chr17:76552611..81041938 [GRCh37]
Chr17:17q25.3		 likely pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:8547-81060040)x3 copy number gain not provided [RCV000739324] Chr17:8547..81060040 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:7214-81058310)x3 copy number gain not provided [RCV000739320] Chr17:7214..81058310 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:12344-81057996)x3 copy number gain not provided [RCV000739325] Chr17:12344..81057996 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
NM_003655.3(CBX4):c.1565C>T (p.Ala522Val) single nucleotide variant Inborn genetic diseases [RCV003271713] Chr17:79834077 [GRCh38]
Chr17:77807876 [GRCh37]
Chr17:17q25.3		 uncertain significance
GRCh37/hg19 17q24.1-25.3(chr17:62778720-81041938)x3 copy number gain not provided [RCV000849900] Chr17:62778720..81041938 [GRCh37]
Chr17:17q24.1-25.3		 pathogenic
GRCh37/hg19 17q25.3(chr17:77067571-77979203)x3 copy number gain not provided [RCV000847213] Chr17:77067571..77979203 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.1183C>G (p.His395Asp) single nucleotide variant Inborn genetic diseases [RCV003290856] Chr17:79834459 [GRCh38]
Chr17:77808258 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.413C>T (p.Ala138Val) single nucleotide variant Inborn genetic diseases [RCV003247378] Chr17:79835229 [GRCh38]
Chr17:77809028 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.210G>C (p.Arg70=) single nucleotide variant not provided [RCV000896667] Chr17:79835682 [GRCh38]
Chr17:77809481 [GRCh37]
Chr17:17q25.3		 benign
NM_003655.3(CBX4):c.1515GGC[5] (p.Ala509_Ala510dup) microsatellite not provided [RCV000948456] Chr17:79834118..79834119 [GRCh38]
Chr17:77807917..77807918 [GRCh37]
Chr17:17q25.3		 benign
GRCh37/hg19 17q25.1-25.3(chr17:73261871-78608763)x3 copy number gain not provided [RCV001006919] Chr17:73261871..78608763 [GRCh37]
Chr17:17q25.1-25.3		 pathogenic
GRCh37/hg19 17q25.3(chr17:77641336-79465235) copy number gain not specified [RCV002052607] Chr17:77641336..79465235 [GRCh37]
Chr17:17q25.3		 uncertain significance
NC_000017.10:g.(?_76851749)_(78367298_?)dup duplication Pityriasis rubra pilaris [RCV003122634] Chr17:76851749..78367298 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.1200C>A (p.His400Gln) single nucleotide variant Inborn genetic diseases [RCV003255011] Chr17:79834442 [GRCh38]
Chr17:77808241 [GRCh37]
Chr17:17q25.3		 uncertain significance
GRCh37/hg19 17q25.1-25.3(chr17:73481509-81043199)x3 copy number gain not provided [RCV002276051] Chr17:73481509..81043199 [GRCh37]
Chr17:17q25.1-25.3		 pathogenic
NM_003655.3(CBX4):c.1676C>T (p.Thr559Met) single nucleotide variant Inborn genetic diseases [RCV002684535] Chr17:79833966 [GRCh38]
Chr17:77807765 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.1453G>A (p.Gly485Arg) single nucleotide variant Inborn genetic diseases [RCV002840696] Chr17:79834189 [GRCh38]
Chr17:77807988 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.1609T>C (p.Phe537Leu) single nucleotide variant Inborn genetic diseases [RCV002836910] Chr17:79834033 [GRCh38]
Chr17:77807832 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.637C>A (p.Pro213Thr) single nucleotide variant Inborn genetic diseases [RCV002662017] Chr17:79835005 [GRCh38]
Chr17:77808804 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.1191C>G (p.His397Gln) single nucleotide variant Inborn genetic diseases [RCV002977136] Chr17:79834451 [GRCh38]
Chr17:77808250 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.859G>A (p.Gly287Arg) single nucleotide variant Inborn genetic diseases [RCV002844246] Chr17:79834783 [GRCh38]
Chr17:77808582 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.1003G>A (p.Val335Ile) single nucleotide variant Inborn genetic diseases [RCV002869663] Chr17:79834639 [GRCh38]
Chr17:77808438 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.940G>C (p.Ala314Pro) single nucleotide variant Inborn genetic diseases [RCV002706794] Chr17:79834702 [GRCh38]
Chr17:77808501 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.1648C>T (p.Leu550Phe) single nucleotide variant Inborn genetic diseases [RCV002797938] Chr17:79833994 [GRCh38]
Chr17:77807793 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.893C>T (p.Ala298Val) single nucleotide variant Inborn genetic diseases [RCV002769785] Chr17:79834749 [GRCh38]
Chr17:77808548 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.280A>T (p.Thr94Ser) single nucleotide variant Inborn genetic diseases [RCV002934864] Chr17:79835362 [GRCh38]
Chr17:77809161 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.209G>A (p.Arg70Gln) single nucleotide variant Inborn genetic diseases [RCV002940620] Chr17:79835683 [GRCh38]
Chr17:77809482 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.1343C>T (p.Pro448Leu) single nucleotide variant Inborn genetic diseases [RCV002854775] Chr17:79834299 [GRCh38]
Chr17:77808098 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.1387A>T (p.Ile463Phe) single nucleotide variant Inborn genetic diseases [RCV003257376] Chr17:79834255 [GRCh38]
Chr17:77808054 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.1357C>T (p.Pro453Ser) single nucleotide variant Inborn genetic diseases [RCV003197172] Chr17:79834285 [GRCh38]
Chr17:77808084 [GRCh37]
Chr17:17q25.3		 uncertain significance
NM_003655.3(CBX4):c.1310C>T (p.Thr437Ile) single nucleotide variant Inborn genetic diseases [RCV003184240] Chr17:79834332 [GRCh38]
Chr17:77808131 [GRCh37]
Chr17:17q25.3		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1481
Count of miRNA genes:731
Interacting mature miRNAs:851
Transcripts:ENST00000269397, ENST00000448310, ENST00000494546, ENST00000495122
Prediction methods:Miranda, Rnahybrid
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.

Markers in Region
RH78479  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371777,807,209 - 77,807,380UniSTSGRCh37
Build 361775,421,804 - 75,421,975RGDNCBI36
Celera1774,433,691 - 74,433,862RGD
Cytogenetic Map17q25.3UniSTS
HuRef1773,248,039 - 73,248,210UniSTS
GeneMap99-GB4 RH Map17521.47UniSTS
NCBI RH Map17810.0UniSTS


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 sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 1573 2146 1523 457 1785 307 2952 768 3073 245 1198 1574 165 1 825 1784 6 2
Low 866 844 203 167 166 158 1405 1426 661 174 262 39 10 379 1004
Below cutoff 1 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_003655 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011525399 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054317610 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC100791 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF013956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI796748 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY390430 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC014967 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BG029608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BQ225831 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068261 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU439707 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KT584485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KU178422 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KU178423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U94344 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000269397   ⟹   ENSP00000269397
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1779,833,156 - 79,839,440 (-)Ensembl
RefSeq Acc Id: ENST00000448310   ⟹   ENSP00000415348
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1779,835,044 - 79,839,387 (-)Ensembl
RefSeq Acc Id: ENST00000494546
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1779,837,746 - 79,839,413 (-)Ensembl
RefSeq Acc Id: ENST00000495122   ⟹   ENSP00000461198
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1779,835,143 - 79,837,881 (-)Ensembl
RefSeq Acc Id: NM_003655   ⟹   NP_003646
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381779,833,156 - 79,839,440 (-)NCBI
GRCh371777,806,955 - 77,813,222 (-)NCBI
Build 361775,421,550 - 75,427,808 (-)NCBI Archive
HuRef1773,247,786 - 73,258,221 (-)ENTREZGENE
CHM1_11777,893,186 - 77,899,450 (-)NCBI
T2T-CHM13v2.01780,730,965 - 80,737,249 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011525399   ⟹   XP_011523701
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381779,833,156 - 79,836,180 (-)NCBI
Sequence:
RefSeq Acc Id: XM_054317610   ⟹   XP_054173585
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01780,730,965 - 80,735,634 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_003646   ⟸   NM_003655
- UniProtKB: Q6TPI8 (UniProtKB/Swiss-Prot),   B1PJR7 (UniProtKB/Swiss-Prot),   Q96C04 (UniProtKB/Swiss-Prot),   O00257 (UniProtKB/Swiss-Prot),   A0A0S2Z5B2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011523701   ⟸   XM_011525399
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSP00000269397   ⟸   ENST00000269397
RefSeq Acc Id: ENSP00000461198   ⟸   ENST00000495122
RefSeq Acc Id: ENSP00000415348   ⟸   ENST00000448310
RefSeq Acc Id: XP_054173585   ⟸   XM_054317610
- Peptide Label: isoform X1
Protein Domains
Chromo

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O00257-F1-model_v2 AlphaFold O00257 1-560 view protein structure

Promoters
RGD ID:6815217
Promoter ID:HG_MRA:7122
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3
Transcripts:CR616461,   U94344
Position:
Human AssemblyChrPosition (strand)Source
Build 361775,421,996 - 75,422,496 (-)MPROMDB
RGD ID:6811135
Promoter ID:HG_ACW:36682
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562,   Lymphoblastoid
Transcripts:CBX4.EAPR07
Position:
Human AssemblyChrPosition (strand)Source
Build 361775,424,601 - 75,425,397 (-)MPROMDB
RGD ID:6793840
Promoter ID:HG_KWN:27304
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:OTTHUMT00000318010
Position:
Human AssemblyChrPosition (strand)Source
Build 361775,425,836 - 75,427,122 (-)MPROMDB
RGD ID:6793844
Promoter ID:HG_KWN:27305
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000343048,   OTTHUMT00000318007,   OTTHUMT00000318008,   OTTHUMT00000318009
Position:
Human AssemblyChrPosition (strand)Source
Build 361775,427,606 - 75,428,106 (-)MPROMDB
RGD ID:7236551
Promoter ID:EPDNEW_H24020
Type:initiation region
Name:CBX4_1
Description:chromobox 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381779,839,440 - 79,839,500EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:1554 AgrOrtholog
COSMIC CBX4 COSMIC
Ensembl Genes ENSG00000141582 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000269397 ENTREZGENE
  ENST00000269397.9 UniProtKB/Swiss-Prot
  ENST00000448310.1 UniProtKB/TrEMBL
  ENST00000495122.1 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000141582 GTEx
HGNC ID HGNC:1554 ENTREZGENE
Human Proteome Map CBX4 Human Proteome Map
InterPro CBX4 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_dom_subgr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromo_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromodomain_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:8535 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 8535 ENTREZGENE
OMIM 603079 OMIM
PANTHER E3 SUMO-PROTEIN LIGASE CBX4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR46727 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CBX7_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromo UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA26129 PharmGKB
PRINTS CHROMODOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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 A0A0S2Z4Q9_HUMAN UniProtKB/TrEMBL
  A0A0S2Z5B2 ENTREZGENE, UniProtKB/TrEMBL
  B1PJR7 ENTREZGENE
  CBX4_HUMAN UniProtKB/Swiss-Prot
  F8WCW6_HUMAN UniProtKB/TrEMBL
  I3L4F1_HUMAN UniProtKB/TrEMBL
  O00257 ENTREZGENE
  Q6TPI8 ENTREZGENE
  Q96C04 ENTREZGENE
UniProt Secondary B1PJR7 UniProtKB/Swiss-Prot
  Q6TPI8 UniProtKB/Swiss-Prot
  Q96C04 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-01 CBX4  chromobox 4    chromobox homolog 4  Symbol and/or name change 5135510 APPROVED
2011-07-27 CBX4  chromobox homolog 4  CBX4  chromobox homolog 4 (Pc class homolog, Drosophila)  Symbol and/or name change 5135510 APPROVED