Hmgb2 high mobility group box 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hmgb2provided by RGD
Official Full Name: high mobility group box 2provided by RGD
Primary source: RGD:69291
See related: EnsemblRapid:ENSRNOG00000013167 AllianceGenome:RGD:69291
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Hmg2
Summary: Enables lipid binding activity. Involved in animal organ regeneration; nervous system development; and positive regulation of nucleobase-containing compound metabolic process. Predicted to be located in several cellular components, including chromosome; nuclear lumen; and perinuclear region of cytoplasm. Predicted to be part of protein-containing complex. Orthologous to human HMGB2 (high mobility group box 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 2007.3), Spleen (RPKM 1198.6) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 16p11

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (37721374..37723950, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (32710651..32713230, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (36077615..36080191, complement)

Chromosome 16 - NC_086034.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HMGB2 Release Promotes Pulmonary Hypertension and Predicts Severity and Mortality of Patients With Pulmonary Arterial Hypertension.
Title: HMGB2 Release Promotes Pulmonary Hypertension and Predicts Severity and Mortality of Patients With Pulmonary Arterial Hypertension.
Downregulation of High mobility group box 2 relieves spinal cord injury by inhibiting microglia-mediated neuroinflammation.
Title: Downregulation of High mobility group box 2 relieves spinal cord injury by inhibiting microglia-mediated neuroinflammation.
the enhance expression of HMGB2 induces the adipogenesis of MSCs and the fat infiltration into skeletal muscles through the cascade of HMGB2-PDGFRA
Title: HMGB2 is a novel adipogenic factor that regulates ectopic fat infiltration in skeletal muscles.
Alteration of the in vitro acetylation pattern of high mobility group box protein-2 and its truncated form lacking the C-terminal tail by CREB-binding protein (CBP)is regarded as a means by which the acidic domain modulates some properties of HGMB2.
Title: In vitro acetylation of HMGB-1 and -2 proteins by CBP: the role of the acidic tail.

Submit: New GeneRIF Correction

General gene information

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Markers

NoName (e-PCR)
- UniSTS:224572

RH126943 (e-PCR)
- UniSTS:209768

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables DNA binding, bending	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding, bending	ISO Inferred from Sequence Orthology more info
enables DNA binding, bending	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables RAGE receptor binding	ISO Inferred from Sequence Orthology more info
enables chemoattractant activity	ISO Inferred from Sequence Orthology more info
enables cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables damaged DNA binding	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables double-stranded DNA binding	TAS Traceable Author Statement more info	PubMed
enables lipid binding	IDA Inferred from Direct Assay more info	PubMed
enables non-sequence-specific DNA binding, bending	ISO Inferred from Sequence Orthology more info
enables non-sequence-specific DNA binding, bending	ISS Inferred from Sequence or Structural Similarity more info
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables single-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables single-stranded DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables supercoiled DNA binding	ISO Inferred from Sequence Orthology more info
enables supercoiled DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA recombination	IEA Inferred from Electronic Annotation more info
involved_in DNA topological change	ISO Inferred from Sequence Orthology more info
involved_in DNA topological change	ISS Inferred from Sequence or Structural Similarity more info
involved_in animal organ regeneration	IEP Inferred from Expression Pattern more info	PubMed
involved_in cell chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in defense response to Gram-negative bacterium	ISO Inferred from Sequence Orthology more info
involved_in defense response to Gram-negative bacterium	ISS Inferred from Sequence or Structural Similarity more info
involved_in defense response to Gram-positive bacterium	ISO Inferred from Sequence Orthology more info
involved_in defense response to Gram-positive bacterium	ISS Inferred from Sequence or Structural Similarity more info
involved_in double-strand break repair via nonhomologous end joining	ISO Inferred from Sequence Orthology more info
acts_upstream_of extrinsic apoptotic signaling pathway via death domain receptors	ISO Inferred from Sequence Orthology more info
involved_in inflammatory response to antigenic stimulus	ISO Inferred from Sequence Orthology more info
involved_in inflammatory response to antigenic stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within male gonad development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in nervous system development	IDA Inferred from Direct Assay more info	PubMed
involved_in nucleosome assembly	ISO Inferred from Sequence Orthology more info
involved_in positive chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA ligase activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of endothelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of erythrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of innate immune response	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interferon-beta production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of megakaryocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of neurogenesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of neurogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of stem cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of stem cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in response to lipopolysaccharide	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within response to steroid hormone	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spermatid nucleus differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spermatogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in chromatin	ISS Inferred from Sequence or Structural Similarity more info
located_in condensed chromosome	ISO Inferred from Sequence Orthology more info
located_in condensed chromosome	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info
located_in extracellular space	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: high mobility group protein B2

Names: HMG-2; high mobility group protein 2

NCBI Reference Sequences (RefSeq)

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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)

NM_017187.2 → NP_058883.1 high mobility group protein B2

See identical proteins and their annotated locations for NP_058883.1

Status: VALIDATED

Source sequence(s)

BC089854

UniProtKB/Swiss-Prot

P52925, Q5FVP0

UniProtKB/TrEMBL

A6KIU7, D3ZN59

Conserved Domains (2) summary

pfam00505
Location:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086034.1 Reference GRCr8

Range

37721374..37723950 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017600052.3 → XP_017455541.1 high mobility group protein B2 isoform X1

UniProtKB/Swiss-Prot

P52925, Q5FVP0

UniProtKB/TrEMBL

A6KIU7, D3ZN59

Related

ENSRNOP00000017635.4, ENSRNOT00000017635.8

Conserved Domains (2) summary

pfam00505
Location:95 → 162

HMG_box; HMG (high mobility group) box

pfam09011
Location:6 → 78

HMG_box_2; HMG-box domain