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ZNF506 zinc finger protein 506 [ Homo sapiens (human) ]

Gene ID: 440515, updated on 2-Nov-2024

Summary

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Official Symbol
ZNF506provided by HGNC
Official Full Name
zinc finger protein 506provided by HGNC
Primary source
HGNC:HGNC:23780
See related
Ensembl:ENSG00000081665 AllianceGenome:HGNC:23780
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of DNA-templated transcription. Located in nucleolus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in thyroid (RPKM 8.8), lymph node (RPKM 4.7) and 25 other tissues See more
Orthologs
all
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Genomic context

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See ZNF506 in Genome Data Viewer
Location:
19p13.11
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (19792711..19821750, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19930412..19959452, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (19903520..19932559, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101060187 Neighboring gene sorting nexin 18 pseudogene Neighboring gene long intergenic non-protein coding RNA 663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14370 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:19887366-19888257 Neighboring gene zinc finger protein 56, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14372 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:19932265-19932779 Neighboring gene iron-sulfur cluster assembly 1 pseudogene 5 Neighboring gene BCL2 interacting protein 3 pseudogene 9

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Unraveling the role of ZNF506 as a human PBS-pro-targeting protein for ERVP repression. Wu Q, et al. Nucleic Acids Res, 2023 Oct 27. PMID 37697430, Free PMC Article
  2. ZNF506-dependent positive feedback loop regulates H2AX signaling after DNA damage. Nowsheen S, et al. Nat Commun, 2018 Jul 16. PMID 30013081, Free PMC Article
  3. PML-associated repressor of transcription (PAROT), a novel KRAB-zinc finger repressor, is regulated through association with PML nuclear bodies. Fleischer S, et al. Exp Cell Res, 2006 Apr 1. PMID 16412420
  4. ARHGAP24 represses β-catenin transactivation-induced invasiveness in hepatocellular carcinoma mainly by acting as a GTPase-independent scaffold. Yang W, et al. Theranostics, 2022. PMID 36168627, Free PMC Article
  5. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. Simpson JC, et al. EMBO Rep, 2000 Sep. PMID 11256614, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Unraveling the role of ZNF506 as a human PBS-pro-targeting protein for ERVP repression.
    Title: Unraveling the role of ZNF506 as a human PBS-pro-targeting protein for ERVP repression.
  2. ZNF506-dependent positive feedback loop regulates H2AX signaling after DNA damage.
    Title: ZNF506-dependent positive feedback loop regulates H2AX signaling after DNA damage.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC27136, DKFZp761G1812

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleolus IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
zinc finger protein 506

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_001099269.3 → NP_001092739.1  zinc finger protein 506 isoform 1

    See identical proteins and their annotated locations for NP_001092739.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC011477, AI559570, AK095575, DA122515
    Consensus CDS
    CCDS42531.1
    UniProtKB/Swiss-Prot
    B3KTH6, Q5JVG8
    Related
    ENSP00000440625.1, ENST00000540806.7
    Conserved Domains (5) summary
    smart00349
    Location:4 → 62
    KRAB; krueppel associated box
    COG5048
    Location:255 → 417
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:259 → 279
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:6 → 43
    KRAB; KRAB box
    pfam13465
    Location:215 → 240
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001145404.2 → NP_001138876.1  zinc finger protein 506 isoform 2

    See identical proteins and their annotated locations for NP_001138876.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AC011477, AI559570, AK095575, AK122848
    Consensus CDS
    CCDS46027.1
    UniProtKB/Swiss-Prot
    Q5JVG8
    Related
    ENSP00000408892.1, ENST00000450683.6
    Conserved Domains (5) summary
    smart00349
    Location:4 → 43
    KRAB; krueppel associated box
    COG5048
    Location:223 → 385
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:227 → 247
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:6 → 43
    KRAB; KRAB box
    pfam13465
    Location:183 → 208
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    19792711..19821750 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    19930412..19959452 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001145405.1: Suppressed sequence

    Description
    NM_001145405.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5JVG8.2 GenPept UniProtKB/Swiss-Prot:Q5JVG8

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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