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Cbx5 chromobox 5 [ Mus musculus (house mouse) ]

Gene ID: 12419, updated on 22-Mar-2020

Summary

Official Symbol
Cbx5provided by MGI
Official Full Name
chromobox 5provided by MGI
Primary source
MGI:MGI:109372
See related
Ensembl:ENSMUSG00000009575
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
HP1; Hp1a; C75991; Hp1alpha; 2610029O15Rik
Expression
Broad expression in CNS E11.5 (RPKM 47.5), whole brain E14.5 (RPKM 29.9) and 22 other tissues See more
Orthologs

Genomic context

See Cbx5 in Genome Data Viewer
Location:
15; 15 F3
Exon count:
7
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (103191546..103239904, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 15 NC_000081.5 (103021977..103070247, complement)

Chromosome 15 - NC_000081.6Genomic Context describing neighboring genes Neighboring gene Riken cDNA D930007P13 gene Neighboring gene single-strand selective monofunctional uracil DNA glycosylase Neighboring gene heterogeneous nuclear ribonucleoprotein A1 Neighboring gene nuclear factor, erythroid derived 2

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase binding IPI
Inferred from Physical Interaction
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
identical protein binding ISO
Inferred from Sequence Orthology
more info
 
methylated histone binding IPI
Inferred from Physical Interaction
more info
PubMed 
methylated histone binding ISO
Inferred from Sequence Orthology
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding, bridging IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
 
repressing transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
ribonucleoprotein complex binding ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
colocalizes_with PML body ISO
Inferred from Sequence Orthology
more info
 
chromocenter IDA
Inferred from Direct Assay
more info
PubMed 
chromosome IEA
Inferred from Electronic Annotation
more info
 
chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
 
heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase complex IDA
Inferred from Direct Assay
more info
PubMed 
histone methyltransferase complex IDA
Inferred from Direct Assay
more info
PubMed 
kinetochore IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
nuclear heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus ISO
Inferred from Sequence Orthology
more info
 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 
pericentric heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex ISO
Inferred from Sequence Orthology
more info
 
ribonucleoprotein complex ISO
Inferred from Sequence Orthology
more info
 
site of DNA damage ISO
Inferred from Sequence Orthology
more info
 
transcriptional repressor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
chromobox protein homolog 5
Names
HP1 alpha
chromobox homolog 5
heterochromatin protein 1 alpha
heterochromatin protein 1 homolog alpha
mHP1(alpha)

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001076789.2NP_001070257.1  chromobox protein homolog 5

    See identical proteins and their annotated locations for NP_001070257.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC162693, AC164069
    Consensus CDS
    CCDS37231.1
    UniProtKB/Swiss-Prot
    Q61686
    Related
    ENSMUSP00000113157.1, ENSMUST00000118152.7
    Conserved Domains (2) summary
    cd18651
    Location:1968
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha
  2. NM_001110216.1NP_001103686.1  chromobox protein homolog 5

    See identical proteins and their annotated locations for NP_001103686.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC162693, AC164069, AK030366, AK030442, BM247903
    Consensus CDS
    CCDS37231.1
    UniProtKB/Swiss-Prot
    Q61686
    Related
    ENSMUSP00000113158.1, ENSMUST00000122182.1
    Conserved Domains (2) summary
    cd18651
    Location:1968
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha
  3. NM_001358950.1NP_001345879.1  chromobox protein homolog 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC162693, AC164069
    Consensus CDS
    CCDS37231.1
    Conserved Domains (2) summary
    cd18651
    Location:1968
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha
  4. NM_007626.3NP_031652.1  chromobox protein homolog 5

    See identical proteins and their annotated locations for NP_031652.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the same protein as variants 2, 3 and 4.
    Source sequence(s)
    AC162693, AC164069
    Consensus CDS
    CCDS37231.1
    UniProtKB/Swiss-Prot
    Q61686
    Related
    ENSMUSP00000104441.3, ENSMUST00000108813.9
    Conserved Domains (2) summary
    cd18651
    Location:1968
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 108 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm38.p6 C57BL/6J

Genomic

  1. NC_000081.6 Reference GRCm38.p6 C57BL/6J

    Range
    103191546..103239904 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006520372.4XP_006520435.1  chromobox protein homolog 5 isoform X1

    See identical proteins and their annotated locations for XP_006520435.1

    UniProtKB/Swiss-Prot
    Q61686
    Conserved Domains (2) summary
    cd18651
    Location:1968
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha
  2. XM_030248308.1XP_030104168.1  chromobox protein homolog 5 isoform X1

  3. XM_006520376.3XP_006520439.1  chromobox protein homolog 5 isoform X1

    See identical proteins and their annotated locations for XP_006520439.1

    UniProtKB/Swiss-Prot
    Q61686
    Conserved Domains (2) summary
    cd18651
    Location:1968
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha
  4. XM_006520374.3XP_006520437.1  chromobox protein homolog 5 isoform X1

    See identical proteins and their annotated locations for XP_006520437.1

    UniProtKB/Swiss-Prot
    Q61686
    Conserved Domains (2) summary
    cd18651
    Location:1968
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha
  5. XM_006520375.4XP_006520438.1  chromobox protein homolog 5 isoform X1

    See identical proteins and their annotated locations for XP_006520438.1

    UniProtKB/Swiss-Prot
    Q61686
    Conserved Domains (2) summary
    cd18651
    Location:1968
    CD_HP1alpha_Cbx5; chromodomain of heterochromatin protein 1 homolog alpha
    cd18655
    Location:116173
    CSD_HP1alpha_Cbx5; chromo shadow domain of heterochromatin protein 1 homolog alpha
  6. XM_006520377.2XP_006520440.1  chromobox protein homolog 5 isoform X2

    Conserved Domains (2) summary
    pfam00385
    Location:2169
    Chromo; Chromo (CHRromatin Organization MOdifier) domain
    cl00044
    Location:115142
    ChSh; Chromo Shadow Domain, found in association with N-terminal chromo (CHRromatin Organization MOdifier) domain; Chromo domains mediate the interaction of the heterochromatin with other heterochromatin proteins, thereby affecting chromatin structure (e.g. ...
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