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hmgn3 high mobility group nucleosomal binding domain 3 [ Danio rerio (zebrafish) ]

Gene ID: 492345, updated on 17-Aug-2024

Summary

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Official Symbol
hmgn3provided by ZNC
Official Full Name
high mobility group nucleosomal binding domain 3provided by ZNC
Primary source
ZFIN:ZDB-GENE-041114-180
See related
Ensembl:ENSDARG00000036754 AllianceGenome:ZFIN:ZDB-GENE-041114-180
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
trip7; fa04b03; zgc:92355; wu:fa04b03
Summary
Predicted to enable chromatin binding activity. Predicted to be involved in chromatin organization. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II and regulation of insulin secretion involved in cellular response to glucose stimulus. Predicted to be located in chromatin. Predicted to be active in nucleus. Is expressed in central nervous system; lens; mucus secreting cell; and otic placode. Orthologous to human HMGN3 (high mobility group nucleosomal binding domain 3). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 23
Exon count:
7
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (31358085..31372807, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 23 NC_007134.6 (31431554..31446276, complement)

Chromosome 23 - NC_007134.7Genomic Context describing neighboring genes Neighboring gene si:dkey-261l7.2 Neighboring gene pleckstrin homology domain interacting protein Neighboring gene si:dkeyp-79f12.7 Neighboring gene lebercilin LCA5

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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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Related articles in PubMed

  1. Knockdown screening of chromatin binding and regulatory proteins in zebrafish identified Suz12b as a regulator of tfpia and an antithrombotic drug target. Raman R, et al. Sci Rep, 2021 Jul 27. PMID 34315984, Free PMC Article
  2. Unexpected novel relational links uncovered by extensive developmental profiling of nuclear receptor expression. Bertrand S, et al. PLoS Genet, 2007 Nov. PMID 17997606, Free PMC Article
  3. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nucleosomal DNA binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in chromatin organization IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of chromatin IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
high mobility group nucleosome-binding domain-containing protein 3

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)

  1. NM_001007311.2 → NP_001007312.1  high mobility group nucleosome-binding domain-containing protein 3 isoform 3

    See identical proteins and their annotated locations for NP_001007312.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 3' coding region that causes a frameshift, compared to variant 1. The resulting protein (isoform 3) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    CR735144, CT617184, EH590201
    UniProtKB/TrEMBL
    A0A8M1N2W1, Q5U381
    Related
    ENSDARP00000053366.6, ENSDART00000053367.8

  2. NM_001243173.1 → NP_001230102.1  high mobility group nucleosome-binding domain-containing protein 3 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    CR735144
    UniProtKB/TrEMBL
    A0A8M1P318, E9QH74
    Related
    ENSDARP00000113097.1, ENSDART00000135620.2

  3. NM_001243174.1 → NP_001230103.1  high mobility group nucleosome-binding domain-containing protein 3 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region compared to variant 1. The resulting protein (isoform 2) is shorter but has the same N- and C-termini compared to isoform 1.
    Source sequence(s)
    CR735144
    UniProtKB/TrEMBL
    A0A8M1NZ58

  4. NM_001243176.1 → NP_001230105.1  high mobility group nucleosome-binding domain-containing protein 3 isoform 4

    See identical proteins and their annotated locations for NP_001230105.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site and lacks an exon in the 3' coding region that causes a frameshift, compared to variant 1. The resulting protein (isoform 4) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    CR735144, CT617184, EH439229, EH475164
    UniProtKB/TrEMBL
    A7YYD1

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007134.7 Reference GRCz11 Primary Assembly

    Range
    31358085..31372807 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018395159.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    193817..209207 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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