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) Sus scrofa
Analyze
Symbol: CBX3
Name: chromobox 3
RGD ID: 13894376
Description: ENCODES a protein that exhibits DNA-binding transcription factor binding (ortholog); transcription cis-regulatory region binding (ortholog); INVOLVED IN cellular response to dexamethasone stimulus (ortholog); negative regulation of DNA-templated transcription (ortholog); ASSOCIATED WITH Habitual Abortions (ortholog); pleomorphic xanthoastrocytoma (ortholog); prostate cancer (ortholog); FOUND IN chromocenter (ortholog); chromosome, centromeric region (ortholog); condensed chromosome, centromeric region (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: chromobox protein homolog 3
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:14681463   PMID:15679890   PMID:17145712   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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 Ensembl4162,337,682 - 162,338,233 (-)EnsemblmRatBN7.2 Ensembl
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
(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
(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
222 total Variants

Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
hemolymphoid system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
10 4 23 3 2 5 14 12 23 3 6 3

Sequence


Ensembl Acc Id: ENSSSCT00000018192   ⟹   ENSSSCP00000017701
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1846,193,140 - 46,204,368 (-)Ensembl
Ensembl Acc Id: ENSSSCT00000051760   ⟹   ENSSSCP00000049786
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1846,193,140 - 46,204,714 (-)Ensembl
Ensembl Acc Id: ENSSSCT00000052029   ⟹   ENSSSCP00000049772
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1846,193,143 - 46,204,540 (-)Ensembl
RefSeq Acc Id: XM_003360191   ⟹   XP_003360239
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11846,193,138 - 46,204,535 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005673310   ⟹   XP_005673367
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11846,193,138 - 46,205,112 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005673311   ⟹   XP_005673368
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11846,193,138 - 46,204,292 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021078986   ⟹   XP_020934645
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11846,193,138 - 46,205,114 (-)NCBI
Sequence:
RefSeq Acc Id: XP_020934645   ⟸   XM_021078986
- Peptide Label: isoform X2
- UniProtKB: F1ST98 (UniProtKB/TrEMBL),   A0A4X1U0R7 (UniProtKB/TrEMBL),   A0A8D1YI68 (UniProtKB/TrEMBL),   A0A8D0KAK1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005673367   ⟸   XM_005673310
- Peptide Label: isoform X1
- UniProtKB: A0A287B0T7 (UniProtKB/TrEMBL),   A0A4X1TVI4 (UniProtKB/TrEMBL),   A0A8D1YI68 (UniProtKB/TrEMBL),   A0A8D0K0G2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_003360239   ⟸   XM_003360191
- Peptide Label: isoform X1
- UniProtKB: A0A287B0T7 (UniProtKB/TrEMBL),   A0A4X1TVI4 (UniProtKB/TrEMBL),   A0A8D1YI68 (UniProtKB/TrEMBL),   A0A8D0K0G2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005673368   ⟸   XM_005673311
- Peptide Label: isoform X1
- UniProtKB: A0A287B0T7 (UniProtKB/TrEMBL),   A0A4X1TVI4 (UniProtKB/TrEMBL),   A0A8D1YI68 (UniProtKB/TrEMBL),   A0A8D0K0G2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSSSCP00000049786   ⟸   ENSSSCT00000051760
Ensembl Acc Id: ENSSSCP00000049772   ⟸   ENSSSCT00000052029
Ensembl Acc Id: ENSSSCP00000017701   ⟸   ENSSSCT00000018192
Protein Domains
Chromo


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000016711 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00015062755 UniProtKB/TrEMBL
  ENSSSCG00065031924 UniProtKB/TrEMBL
  ENSSSCG00070013008 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000018192 ENTREZGENE
  ENSSSCT00000018192.5 UniProtKB/TrEMBL
  ENSSSCT00000051760.3 UniProtKB/TrEMBL
  ENSSSCT00000052029 ENTREZGENE
  ENSSSCT00000052029.3 UniProtKB/TrEMBL
  ENSSSCT00015084018.1 UniProtKB/TrEMBL
  ENSSSCT00065043235.1 UniProtKB/TrEMBL
  ENSSSCT00070025733.1 UniProtKB/TrEMBL
  ENSSSCT00070025751.1 UniProtKB/TrEMBL
  ENSSSCT00070025766.1 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.40 UniProtKB/TrEMBL
InterPro CBX3 UniProtKB/TrEMBL
  Chromo-like_dom_sf UniProtKB/TrEMBL
  Chromo/chromo_shadow_dom UniProtKB/TrEMBL
  Chromo_dom_subgr UniProtKB/TrEMBL
  Chromo_domain UniProtKB/TrEMBL
  Chromo_shadow_dom UniProtKB/TrEMBL
  Chromodomain_CS UniProtKB/TrEMBL
  Heterochromatin_chromo-domain UniProtKB/TrEMBL
KEGG Report ssc:100622432 UniProtKB/TrEMBL
NCBI Gene CBX3 ENTREZGENE
PANTHER CHROMOBOX PROTEIN UniProtKB/TrEMBL
Pfam Chromo UniProtKB/TrEMBL
  Chromo_shadow UniProtKB/TrEMBL
PRINTS CHROMODOMAIN UniProtKB/TrEMBL
PROSITE CHROMO_1 UniProtKB/TrEMBL
  CHROMO_2 UniProtKB/TrEMBL
SMART CHROMO UniProtKB/TrEMBL
  ChSh UniProtKB/TrEMBL
Superfamily-SCOP SSF54160 UniProtKB/TrEMBL
UniProt A0A287B039_PIG UniProtKB/TrEMBL
  A0A287B0T7 ENTREZGENE
  A0A4X1TVI4 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1U0R7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0K0G2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0KAK1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1YI68 ENTREZGENE, UniProtKB/TrEMBL
  F1ST98 ENTREZGENE
UniProt Secondary A0A287B0T7 UniProtKB/TrEMBL
  F1ST98 UniProtKB/TrEMBL