CBX4 (chromobox 4) - Rat Genome Database

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Gene: CBX4 (chromobox 4) Sus scrofa
Analyze
Symbol: CBX4
Name: chromobox 4
RGD ID: 13987660
Description: ENCODES a protein that exhibits SUMO transferase activity (ortholog); INVOLVED IN negative regulation of transcription by RNA polymerase II (ortholog); protein sumoylation (ortholog); PARTICIPATES IN histone modification pathway; ASSOCIATED WITH genetic disease (ortholog); hepatocellular carcinoma (ortholog); Neoplasm Metastasis (ortholog); FOUND IN nuclear body (inferred); nucleoplasm (inferred); nucleus (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: E3 SUMO-protein ligase CBX4
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
69 total Variants

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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 1 1
Low 10 4 3 4 2 23 2 2 3
Below cutoff

Sequence


RefSeq Acc Id: ENSSSCT00000018684   ⟹   ENSSSCP00000018183
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl122,521,027 - 2,527,241 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000055713   ⟹   ENSSSCP00000052507
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl122,520,698 - 2,527,241 (+)Ensembl
RefSeq Acc Id: XM_003131145   ⟹   XP_003131193
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1122,520,913 - 2,527,245 (+)NCBI
Sequence:
RefSeq Acc Id: XP_003131193   ⟸   XM_003131145
- UniProtKB: F1RZ78 (UniProtKB/TrEMBL),   A0A4X1UJ61 (UniProtKB/TrEMBL),   A0A4X1UJ65 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000052507   ⟸   ENSSSCT00000055713
RefSeq Acc Id: ENSSSCP00000018183   ⟸   ENSSSCT00000018684
Protein Domains
Chromo


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000017160 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00025061227 UniProtKB/TrEMBL
  ENSSSCG00030072981 UniProtKB/TrEMBL
  ENSSSCG00035078620 UniProtKB/TrEMBL
  ENSSSCG00040053933 UniProtKB/TrEMBL
  ENSSSCG00045016314 UniProtKB/TrEMBL
  ENSSSCG00050039999 UniProtKB/TrEMBL
  ENSSSCG00055017659 UniProtKB/TrEMBL
  ENSSSCG00060064089 UniProtKB/TrEMBL
  ENSSSCG00065073927 UniProtKB/TrEMBL
  ENSSSCG00070017371 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000018684 ENTREZGENE
  ENSSSCT00000018684.3 UniProtKB/TrEMBL
  ENSSSCT00025083810.1 UniProtKB/TrEMBL
  ENSSSCT00025083946.1 UniProtKB/TrEMBL
  ENSSSCT00025084038.1 UniProtKB/TrEMBL
  ENSSSCT00030102193.1 UniProtKB/TrEMBL
  ENSSSCT00035107295.1 UniProtKB/TrEMBL
  ENSSSCT00035107319.1 UniProtKB/TrEMBL
  ENSSSCT00035107331.1 UniProtKB/TrEMBL
  ENSSSCT00040072919.1 UniProtKB/TrEMBL
  ENSSSCT00040073035.1 UniProtKB/TrEMBL
  ENSSSCT00040073082.1 UniProtKB/TrEMBL
  ENSSSCT00045027757.1 UniProtKB/TrEMBL
  ENSSSCT00045027803.1 UniProtKB/TrEMBL
  ENSSSCT00045027853.1 UniProtKB/TrEMBL
  ENSSSCT00050054034.1 UniProtKB/TrEMBL
  ENSSSCT00055034627.1 UniProtKB/TrEMBL
  ENSSSCT00055034760.1 UniProtKB/TrEMBL
  ENSSSCT00055034818.1 UniProtKB/TrEMBL
  ENSSSCT00060087463.1 UniProtKB/TrEMBL
  ENSSSCT00060087482.1 UniProtKB/TrEMBL
  ENSSSCT00060087492.1 UniProtKB/TrEMBL
  ENSSSCT00065101796.1 UniProtKB/TrEMBL
  ENSSSCT00065101805.1 UniProtKB/TrEMBL
  ENSSSCT00070034277.1 UniProtKB/TrEMBL
  ENSSSCT00070034281.1 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.40 UniProtKB/TrEMBL
InterPro CBX4 UniProtKB/TrEMBL
  CBX7_C UniProtKB/TrEMBL
  Chromo-like_dom_sf UniProtKB/TrEMBL
  Chromo/chromo_shadow_dom UniProtKB/TrEMBL
  Chromo_dom_subgr UniProtKB/TrEMBL
  Chromo_domain UniProtKB/TrEMBL
  Chromodomain_CS UniProtKB/TrEMBL
KEGG Report ssc:100511584 UniProtKB/TrEMBL
NCBI Gene CBX4 ENTREZGENE
PANTHER E3 SUMO-PROTEIN LIGASE CBX4 UniProtKB/TrEMBL
  PTHR46727 UniProtKB/TrEMBL
Pfam CBX7_C UniProtKB/TrEMBL
  Chromo UniProtKB/TrEMBL
PRINTS CHROMODOMAIN UniProtKB/TrEMBL
PROSITE CHROMO_1 UniProtKB/TrEMBL
  CHROMO_2 UniProtKB/TrEMBL
SMART CHROMO UniProtKB/TrEMBL
Superfamily-SCOP SSF54160 UniProtKB/TrEMBL
UniProt A0A4X1UJ61 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1UJ65 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0SU08_PIG UniProtKB/TrEMBL
  F1RZ78 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:86231 ENTREZGENE