hmgb1a high mobility group box 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: hmgb1aprovided by ZNC
Official Full Name: high mobility group box 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-341
See related: Ensembl:ENSDARG00000099175 AllianceGenome:ZFIN:ZDB-GENE-030131-341
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: hmgb1; zgc:56110; zgc:77104; tdsubc_1a5; wu:fb23c02; ik:tdsubc_1a5; xx:tdsubc_1a5
Summary: Predicted to enable DNA binding activity, bending. Acts upstream of or within axon regeneration; forebrain development; and response to cold. Located in plasma membrane. Is expressed in several structures, including blastomere; epidermis; intermediate cell mass of mesoderm; nervous system; and ventral mesoderm. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis and congestive heart failure. Orthologous to human HMGB1 (high mobility group box 1). [provided by Alliance of Genome Resources, Apr 2022]
Annotation information: Annotation category: partial on reference assembly
Orthologs: all
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Genomic context

Location:: chromosome: 10

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	10	NC_007121.7 (36026580..36031374)
105	previous assembly	GRCz10 (GCF_000002035.5)	10	NC_007121.6 (36082822..36087616)

Chromosome 10 - NC_007121.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SCARA5 is an HMGB1 recognition receptor that is negatively involved in HMGB1-mediated inflammation in pufferfish (Tetraodon nigroviridis) and zebrafish (Danio rerio) models.
Title: Scavenger Receptor SCARA5 Acts as an HMGB1 Recognition Molecule Negatively Involved in HMGB1-Mediated Inflammation in Fish Models.
HMGB1 is a critical factor for brain development, enabling survival and proliferation of neural progenitors that will form the forebrain structures.
Title: High mobility group box-1 (HMGB1; amphoterin) is required for zebrafish brain development.

Submit: New GeneRIF Correction

General gene information

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Markers

fa91a04.x1 (e-PCR)
- UniSTS:189619

fa91a04.x1 (e-PCR)
- UniSTS:189620

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding, bending	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within axon regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within forebrain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within response to cold	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: high mobility group protein B1a

Names: high mobility group box 1

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_199555.3 → NP_955849.2 high mobility group protein B1a

See identical proteins and their annotated locations for NP_955849.2

Status: VALIDATED

Source sequence(s)

CABZ01017703

UniProtKB/TrEMBL

Q6NX86, Q6TGZ8

Related

ENSDARP00000153427.1, ENSDART00000193786.1

Conserved Domains (2) summary

pfam00505
Location:94 → 161

HMG_box; HMG (high mobility group) box

cl00082
Location:5 → 77

HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...