Cbx5 (chromobox 5) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Cbx5 (chromobox 5) Ictidomys tridecemlineatus
Analyze
Symbol: Cbx5
Name: chromobox 5
RGD ID: 12666144
Description: ENCODES a protein that exhibits chromatin binding (inferred); DNA-binding transcription factor binding (inferred); histone deacetylase binding (inferred); INVOLVED IN negative regulation of DNA-templated transcription (ortholog); PARTICIPATES IN histone modification pathway; ASSOCIATED WITH Colorectal Neoplasms (ortholog); lung adenocarcinoma (ortholog); Lung Neoplasms (ortholog); FOUND IN chromocenter (inferred); chromosome, telomeric region (inferred); heterochromatin (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: chromobox 5, transcript variant X1; chromobox 5, transcript variant X2; chromobox 5, transcript variant X3; chromobox protein homolog 5
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494561,683,589 - 61,723,060 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651211,450,060 - 11,480,727 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493651211,441,770 - 11,480,924 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Cbx5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494561,683,589 - 61,723,060 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651211,450,060 - 11,480,727 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493651211,441,770 - 11,480,924 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CBX5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381254,230,942 - 54,280,122 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1254,230,942 - 54,280,133 (-)EnsemblGRCh38hg38GRCh38
GRCh371254,624,726 - 54,673,906 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361252,921,677 - 52,960,151 (-)NCBINCBI36Build 36hg18NCBI36
Build 341252,921,677 - 52,960,151NCBI
Celera1254,276,743 - 54,325,894 (-)NCBICelera
Cytogenetic Map12q13.13NCBI
HuRef1251,663,959 - 51,713,186 (-)NCBIHuRef
CHM1_11254,591,455 - 54,640,653 (-)NCBICHM1_1
T2T-CHM13v2.01254,197,516 - 54,246,699 (-)NCBIT2T-CHM13v2.0
Cbx5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915103,099,973 - 103,148,337 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl15103,099,971 - 103,148,243 (-)EnsemblGRCm39 Ensembl
GRCm3815103,191,546 - 103,239,904 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15103,191,544 - 103,239,816 (-)EnsemblGRCm38mm10GRCm38
MGSCv3715103,021,977 - 103,070,247 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3615103,019,130 - 103,043,372 (-)NCBIMGSCv36mm8
Celera15105,352,806 - 105,401,405 (-)NCBICelera
Cytogenetic Map15F3NCBI
cM Map1558.34NCBI
Cbx5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87136,203,827 - 136,254,575 (-)NCBIGRCr8
mRatBN7.27134,333,165 - 134,376,102 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7134,331,335 - 134,375,022 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7136,088,404 - 136,105,880 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07138,317,781 - 138,335,258 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07138,303,847 - 138,321,314 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07144,819,673 - 144,865,014 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,819,420 - 144,837,583 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,605,275 - 142,647,738 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47142,107,922 - 142,125,543 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17142,187,961 - 142,229,833 (-)NCBI
Celera7130,758,832 - 130,776,255 (-)NCBICelera
Cytogenetic Map7q36NCBI
Cbx5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554581,486,951 - 1,505,653 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554581,486,951 - 1,529,649 (-)NCBIChiLan1.0ChiLan1.0
CBX5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21039,891,136 - 39,948,939 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11239,887,905 - 39,945,708 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01234,463,826 - 34,521,656 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11235,189,095 - 35,246,660 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1235,218,239 - 35,236,009 (+)Ensemblpanpan1.1panPan2
CBX5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1271,020,500 - 1,058,027 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl271,039,594 - 1,049,788 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2745,197,396 - 45,234,943 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0271,017,407 - 1,054,956 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl271,017,441 - 1,054,183 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1271,036,373 - 1,073,913 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0271,017,977 - 1,055,663 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02745,601,201 - 45,638,748 (-)NCBIUU_Cfam_GSD_1.0
CBX5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl519,446,086 - 19,484,463 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1519,446,083 - 19,484,527 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2520,290,445 - 20,329,012 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CBX5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11150,350,440 - 50,396,595 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1150,353,638 - 50,396,608 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037195,645,487 - 195,688,609 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cbx5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249042,276,036 - 2,296,706 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249042,273,054 - 2,313,723 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSSTOT00000014670   ⟹   ENSSTOP00000013142
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_00493651211,450,191 - 11,463,508 (-)Ensembl
Ensembl Acc Id: ENSSTOT00000038759   ⟹   ENSSTOP00000031358
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_00493651211,450,060 - 11,480,727 (-)Ensembl
RefSeq Acc Id: XM_005325072   ⟹   XP_005325129
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494561,701,259 - 61,723,060 (+)NCBI
SpeTri2.0NW_00493651211,441,770 - 11,463,513 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005325074   ⟹   XP_005325131
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494561,684,056 - 61,723,060 (+)NCBI
SpeTri2.0NW_00493651211,441,770 - 11,480,924 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021726230   ⟹   XP_021581905
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494561,701,431 - 61,723,060 (+)NCBI
SpeTri2.0NW_00493651211,441,770 - 11,463,399 (-)NCBI
Sequence:
RefSeq Acc Id: XM_040280526   ⟹   XP_040136460
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494561,683,589 - 61,723,060 (+)NCBI
RefSeq Acc Id: XP_005325131   ⟸   XM_005325074
- Peptide Label: isoform X2
- UniProtKB: I3MNC5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005325129   ⟸   XM_005325072
- Peptide Label: isoform X2
- UniProtKB: I3MNC5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_021581905   ⟸   XM_021726230
- Peptide Label: isoform X2
- UniProtKB: I3MNC5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_040136460   ⟸   XM_040280526
- Peptide Label: isoform X1
Ensembl Acc Id: ENSSTOP00000031358   ⟸   ENSSTOT00000038759
Ensembl Acc Id: ENSSTOP00000013142   ⟸   ENSSTOT00000014670
Protein Domains
Chromo


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000014668 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000014670.3 UniProtKB/TrEMBL
  ENSSTOT00000038759.1 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.40 UniProtKB/TrEMBL
InterPro 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
NCBI Gene Cbx5 ENTREZGENE
PANTHER CHROMOBOX PROTEIN UniProtKB/TrEMBL
  CHROMOBOX PROTEIN HOMOLOG 5 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 I3MNC5 ENTREZGENE, UniProtKB/TrEMBL