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

    Gene ID: 440515, updated on 10-Dec-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, Dec 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
    • 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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