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Aliases for HMGN5 Gene

Aliases for HMGN5 Gene

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

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 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 , fRNAdb sequence ontologies and piRNA Summary for HMGN5 Gene

Genomics for HMGN5 Gene

GeneHancer (GH) Regulatory Elements for HMGN5 Gene

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
GH0XI081200 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 550.8 -0.8 -822 3.7 BRCA1 YY1 TCF12 ZNF143 ATF7 ZNF548 IKZF2 SMAD5 ELF1 REST SH3BGRL HMGN5 BRWD3 GC0XP081328
GH0XI081120 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 550.2 +80.6 80642 2.6 PKNOX1 DEAF1 RAD21 YY1 RFX5 ZNF335 ZNF366 SCRT2 FOS CREM HMGN5 BRWD3 LOC100422286 SH3BGRL GC0XP081187 GC0XP081188 GC0XP081189 GC0XP081190 GC0XP081191 PIR53765
GH0XI081208 Enhancer 0.5 ENCODE 0.4 -6.7 -6695 0.2 ZNF217 CTBP1 GATA3 CUX1 FOXA1 TCF7L2 SH3BGRL HMGN5 GC0XP081328
GH0XI081205 Enhancer 0.2 Ensembl 0.8 -3.2 -3159 0.2 SH3BGRL HMGN5 GC0XP081328
GH0XI081206 Enhancer 0.2 Ensembl 0.8 -4.5 -4459 0.4 SH3BGRL HMGN5 GC0XP081328
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HMGN5 on UCSC Golden Path with GeneCards custom track

Genomic Locations for HMGN5 Gene

Genomic Locations for HMGN5 Gene
chrX:81,113,701-81,201,942
(GRCh38/hg38)
Size:
88,242 bases
Orientation:
Minus strand
chrX:80,369,200-80,457,441
(GRCh37/hg19)

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 StructureGene Density

RefSeq DNA sequence for HMGN5 Gene

Proteins for HMGN5 Gene

  • 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; Positions=132; Evidence={ECO:0000305};

neXtProt entry for HMGN5 Gene

Post-translational modifications for HMGN5 Gene

No Post-translational modifications

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

Suggested Antigen Peptide Sequences for HMGN5 Gene

GenScript: Design optimal peptide antigens:

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

Molecular function for HMGN5 Gene

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

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 NAS 11161810
GO:0003723 RNA binding IDA,HDA 22681889
GO:0031492 nucleosomal DNA binding IEA --
genes like me logo Genes that share ontologies with HMGN5: view

Phenotypes for HMGN5 Gene

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

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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
extracellular 1
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

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
genes like me logo Genes that share ontologies with HMGN5: view

Pathways & Interactions for HMGN5 Gene

SuperPathways for HMGN5 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HMGN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated NAS 11161810
GO:0006357 regulation of transcription by RNA polymerase II IBA --
GO:0008284 positive regulation of cell proliferation IMP 20531280
GO:0010628 positive regulation of gene expression 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

No Compound Related Data Available

Transcripts for HMGN5 Gene

Unigene Clusters for HMGN5 Gene

High mobility group nucleosome binding domain 5:
Representative Sequences:

Clone Products

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

No ASD Table

Relevant External Links for HMGN5 Gene

GeneLoc Exon Structure for
HMGN5
ECgene alternative splicing isoforms for
HMGN5

Expression for HMGN5 Gene

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

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, PaxDb, MaxQB, and MOPED for HMGN5 Gene



NURSA nuclear receptor signaling pathways regulating expression of HMGN5 Gene:

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(4.3)
  • Bone marrow(4.2)
genes like me logo Genes that share expression patterns with HMGN5: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , 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 33 34
  • 97.7 (n)
cow
(Bos Taurus)
Mammalia HMGN5 33 34
  • 85.56 (n)
dog
(Canis familiaris)
Mammalia HMGN5 34
  • 49 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hmgn5 34
  • 35 (a)
OneToOne
Species where no ortholog for HMGN5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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)

Paralogs for HMGN5 Gene

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

genes like me logo Genes that share paralogs with HMGN5: view

No data available for Paralogs for HMGN5 Gene

Variants for HMGN5 Gene

Sequence variations from dbSNP and Humsavar for HMGN5 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1000071236 -- 81,199,650(-) G/A/T genic_upstream_transcript_variant, intron_variant
rs1000077159 -- 81,150,004(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000124749 -- 81,198,847(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000178528 -- 81,189,775(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000208398 -- 81,143,792(-) G/T genic_upstream_transcript_variant, intron_variant

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

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

Disorders for HMGN5 Gene

Additional Disease Information for HMGN5

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 58
  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 58
  3. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PMID: 15592455) Rush J … Comb MJ (Nature biotechnology 2005) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  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 58

Products for HMGN5 Gene

Sources for HMGN5 Gene

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