HMGN5 Gene (Protein Coding)

High Mobility Group Nucleosome Binding Domain 5

GC0XM081113
GIFtS:
31
This gene encodes a nuclear protein with similarities to the high mobility group proteins, HMG14 and HMG17, which suggests that this protein may function as a nucleosomal binding and transcriptional activating protein. [provided by RefSeq, Sep 2009] See more...

Aliases for HMGN5 Gene

Aliases for HMGN5 Gene

  • High Mobility Group Nucleosome Binding Domain 5 2 3 5
  • High Mobility Group Nucleosome-Binding Domain-Containing Protein 5 3 4
  • Nucleosomal Binding Protein 1 2 3
  • Nucleosome-Binding Protein 1 3 4
  • NSBP1 3 4
  • High-Mobility Group Nucleosome Binding Domain 5 2
  • NBP-45 3
  • HMGN5 5

External Ids for HMGN5 Gene

Previous HGNC Symbols for HMGN5 Gene

  • NSBP1

Previous GeneCards Identifiers for HMGN5 Gene

  • GC0XM080255
  • GC0XM080370
  • GC0XM073949

Summaries for HMGN5 Gene

Entrez Gene Summary for HMGN5 Gene

  • This gene encodes a nuclear protein with similarities to the high mobility group proteins, HMG14 and HMG17, which suggests that this protein may function as a nucleosomal binding and transcriptional activating protein. [provided by RefSeq, Sep 2009]

GeneCards Summary for HMGN5 Gene

HMGN5 (High Mobility Group Nucleosome Binding Domain 5) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include nucleosomal DNA binding.

UniProtKB/Swiss-Prot Summary for HMGN5 Gene

  • Preferentially binds to euchromatin and modulates cellular transcription by counteracting linker histone-mediated chromatin compaction.

Additional gene information for HMGN5 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HMGN5 Gene

Genomics for HMGN5 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for HMGN5 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH0XJ081120 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 250.2 +80.8 80812 3 TBP SP1 IKZF1 CTCF IRF3 MAX TRIM22 MAFF RAD21 RFX5 HMGN5 SH3BGRL piR-55194-447 RF00017-8550 lnc-BRWD3-1 BRWD3
GH0XJ081200 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 0.7 -2.4 -2388 7 CHD2 TBP IKZF1 SMAD5 BRCA1 ELF1 SIN3A VEZF1 REST ZNF341 SH3BGRL BRWD3 HMGN5 HSALNG0138810 lnc-BRWD3-1 piR-32407-003
GH0XJ081213 Enhancer 0.2 Ensembl 4.9 -11.2 -11188 2.6 HMGN5 HSALNG0138810 SH3BGRL piR-32407-003
GH0XJ081194 Enhancer 0.5 Ensembl 0.4 +6.5 6512 1.6 CTCF TRIM22 SMC3 RAD21 TCF7L2 ZNF660 ZNF143 ZNF654 HMGN5 lnc-BRWD3-1 piR-55194-447 BRWD3
GH0XJ081198 Enhancer 0.3 Ensembl 0.7 +3.9 3912 0.8 PRDM1 HMGN5 lnc-BRWD3-1 piR-55194-447 BRWD3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HMGN5 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HMGN5

Genomic Locations for HMGN5 Gene

Latest Assembly
chrX:81,113,699-81,201,913
(GRCh38/hg38)
Size:
88,215 bases
Orientation:
Minus strand

Previous Assembly
chrX:80,369,198-80,457,412
(GRCh37/hg19 by Entrez Gene)
Size:
88,215 bases
Orientation:
Minus strand

chrX:80,369,200-80,457,441
(GRCh37/hg19 by Ensembl)
Size:
88,242 bases
Orientation:
Minus strand

Genomic View for HMGN5 Gene

Genes around HMGN5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMGN5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMGN5 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HMGN5 Gene

Proteins for HMGN5 Gene

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  1. Antibodies for research
  2. Protein products for research
  3. Assay products for research

  • Protein details for HMGN5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P82970-HMGN5_HUMAN
    Recommended name:
    High mobility group nucleosome-binding domain-containing protein 5
    Protein Accession:
    P82970
    Secondary Accessions:
    • Q5JSL1

    Protein attributes for HMGN5 Gene

    Size:
    282 amino acids
    Molecular mass:
    31525 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AK094058; Type=Frameshift; Evidence={ECO:0000305};

neXtProt entry for HMGN5 Gene

Protein Expression for HMGN5 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for HMGN5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HMGN5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HMGN5 Gene

Domains & Families for HMGN5 Gene

Gene Families for HMGN5 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for HMGN5 Gene

InterPro:
Blocks:
  • High mobility group protein HMG14 and HMG17
ProtoNet:

Suggested Antigen Peptide Sequences for HMGN5 Gene

GenScript: Design optimal peptide antigens:
  • Nucleosome-binding protein 1 (HMGN5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P82970

UniProtKB/Swiss-Prot:

HMGN5_HUMAN :
  • Specifically targeted by its C-terminus to nucleosomes in euchromatin.
  • Belongs to the HMGN family.
Domain:
  • Specifically targeted by its C-terminus to nucleosomes in euchromatin.
Family:
  • Belongs to the HMGN family.
genes like me logo Genes that share domains with HMGN5: view

Function for HMGN5 Gene

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  6. Cell Lines for research

Molecular function for HMGN5 Gene

UniProtKB/Swiss-Prot Function:
Preferentially binds to euchromatin and modulates cellular transcription by counteracting linker histone-mediated chromatin compaction.

Phenotypes From GWAS Catalog for HMGN5 Gene

Gene Ontology (GO) - Molecular Function for HMGN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA,NAS 11161810
GO:0003723 RNA binding HDA 22681889
GO:0031492 nucleosomal DNA binding IEA --
genes like me logo Genes that share ontologies with HMGN5: view

Phenotypes for HMGN5 Gene

GenomeRNAi human phenotypes for HMGN5:
genes like me logo Genes that share phenotypes with HMGN5: view

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMGN5

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HMGN5 Gene

Localization for HMGN5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMGN5 Gene

Nucleus. Note=Associates with nucleosomes in euchromatin and is largely excluded from constitutive heterochromatin. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HMGN5 gene
Compartment Confidence
nucleus 5
mitochondrion 4
extracellular 2
plasma membrane 1
cytoskeleton 1
endoplasmic reticulum 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Mitochondria (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HMGN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IEA --
GO:0005634 nucleus IEA,NAS 11161810
GO:0005654 nucleoplasm IDA --
GO:0005739 mitochondrion IDA --
genes like me logo Genes that share ontologies with HMGN5: view

Pathways & Interactions for HMGN5 Gene

PathCards logo

SuperPathways for HMGN5 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HMGN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006355 regulation of transcription, DNA-templated NAS 11161810
GO:0008284 positive regulation of cell proliferation IMP 20531280
GO:0010628 positive regulation of gene expression IMP 20531280
GO:0043066 negative regulation of apoptotic process IMP 20531280
genes like me logo Genes that share ontologies with HMGN5: view

No data available for Pathways by source and SIGNOR curated interactions for HMGN5 Gene

Drugs & Compounds for HMGN5 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for HMGN5 Gene

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mRNA/cDNA for HMGN5 Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMGN5

Alternative Splicing Database (ASD) splice patterns (SP) for HMGN5 Gene

No ASD Table

Relevant External Links for HMGN5 Gene

GeneLoc Exon Structure for
HMGN5

Expression for HMGN5 Gene

Products:

  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HMGN5 Gene

mRNA expression in normal human tissues for HMGN5 Gene
mRNA expression by GTEx for HMGN5 GenemRNA expression by BioGPS for HMGN5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Testis (Reproductive System)

mRNA differential expression in normal tissues according to GTEx for HMGN5 Gene

This gene is overexpressed in Testis (x6.0).

Protein differential expression in normal tissues from HIPED for HMGN5 Gene

This gene is overexpressed in Liver (16.1), Nasal epithelium (12.2), and Testis (10.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HMGN5 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HMGN5

SOURCE GeneReport for Unigene cluster for HMGN5 Gene:

Hs.282204

mRNA Expression by UniProt/SwissProt for HMGN5 Gene:

P82970-HMGN5_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for HMGN5 Gene

  • Nervous system(4.4)
  • Bone marrow(4.3)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with HMGN5: view

Primer products for research

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for HMGN5 Gene

Orthologs for HMGN5 Gene

This gene was present in the common ancestor of mammals.

Orthologs for HMGN5 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia HMGN5 30 31
  • 97.7 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia HMGN5 30 31
  • 85.56 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia HMGN5 31
  • 49 (a)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Hmgn5 31
  • 35 (a)
 OneToOne
Species where no ortholog for HMGN5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for HMGN5 Gene

ENSEMBL:
Gene Tree for HMGN5 (if available)
TreeFam:
Gene Tree for HMGN5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HMGN5: view image

Paralogs for HMGN5 Gene

(2) SIMAP similar genes for HMGN5 Gene using alignment to 6 proteins:

  • HMGN5_HUMAN
  • Q5JSK6_HUMAN
  • Q5JSK7_HUMAN
  • Q5JSK8_HUMAN
  • Q5JSK9_HUMAN
  • Q5JSL0_HUMAN
genes like me logo Genes that share paralogs with HMGN5: view

No data available for Paralogs for HMGN5 Gene

Variants for HMGN5 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HMGN5 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
rs142173136 Likely Benign: not provided 81,119,810(-) C/A
NM_030763.3(HMGN5):c.23G>T (p.Gly8Val) 		MISSENSE
rs144502161 Benign: not provided 81,115,003(-) C/G
NM_030763.3(HMGN5):c.495G>C (p.Glu165Asp) 		MISSENSE
rs73231013 Benign: not provided 81,118,462(-) C/T
NM_030763.3(HMGN5):c.99G>A (p.Glu33=) 		SYNONYMOUS
rs73631719 Benign: not provided 81,118,482(-) G/A
NM_030763.3(HMGN5):c.79C>T (p.Leu27Phe) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for HMGN5 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for HMGN5 Gene

Variant ID Type Subtype PubMed ID
esv24043 CNV loss 19812545
esv2671958 CNV deletion 23128226
esv3307397 CNV mobile element insertion 20981092
esv33127 CNV loss 17666407
esv3335197 CNV insertion 20981092

Variation tolerance for HMGN5 Gene

Gene Damage Index Score: 2.46; 43.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HMGN5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HMGN5

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HMGN5 Gene

Disorders for HMGN5 Gene

Additional Disease Information for HMGN5

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for HMGN5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HMGN5 Gene

Publications for HMGN5 Gene

  1. Characterization of a human gene encoding nucleosomal binding protein NSBP1. (PMID: 11161810) King LM … Francomano CA (Genomics 2001) 2 3 4
  2. The interaction of NSBP1/HMGN5 with nucleosomes in euchromatin counteracts linker histone-mediated chromatin compaction and modulates transcription. (PMID: 19748358) Rochman M … Bustin M (Molecular cell 2009) 2 3
  3. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PMID: 15592455) Rush J … Comb MJ (Nature biotechnology 2005) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

ExternalLinks

View latest publications for HMGN5 gene in Mastermind

Products for HMGN5 Gene

Sources for HMGN5 Gene