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    ZNF480 zinc finger protein 480 [ Homo sapiens (human) ]

    Gene ID: 147657, updated on 28-Oct-2024

    Summary

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    Official Symbol
    ZNF480provided by HGNC
    Official Full Name
    zinc finger protein 480provided by HGNC
    Primary source
    HGNC:HGNC:23305
    See related
    Ensembl:ENSG00000198464 MIM:613910; AllianceGenome:HGNC:23305
    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 transcription by RNA polymerase II. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 3.1), lymph node (RPKM 2.7) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ZNF480 in Genome Data Viewer
    Location:
    19q13.41
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (52297169..52325922)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (55384358..55413117)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (52800422..52829175)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904763 Neighboring gene Sharpr-MPRA regulatory region 2064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15043 Neighboring gene zinc finger protein 766 Neighboring gene microRNA 643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15045 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:52841280-52841780 Neighboring gene zinc finger protein 610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15048 Neighboring gene zinc finger protein 880 Neighboring gene ZNF528 antisense RNA 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:52900414-52901613

    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. A novel KRAB zinc-finger protein, ZNF480, expresses in human heart and activates transcriptional activities of AP-1 and SRE. Yi Z, et al. Biochem Biophys Res Commun, 2004 Jul 23. PMID 15219843
    2. Investigation of rare variants in LRP1, KPNA1, ALS2CL and ZNF480 genes in schizophrenia patients reflects genetic heterogeneity of the disease. Jouan L, et al. Behav Brain Funct, 2013 Feb 20. PMID 23425335, Free PMC Article
    3. Acetylation-Mimic Mutation of TRIM28-Lys304 to Gln Attenuates the Interaction with KRAB-Zinc-Finger Proteins and Affects Gene Expression in Leukemic K562 Cells. Chang YJ, et al. Int J Mol Sci, 2023 Jun 6. PMID 37372979, Free PMC Article
    4. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. König R, et al. Cell, 2008 Oct 3. PMID 18854154, Free PMC Article
    5. A Y2H-seq approach defines the human protein methyltransferase interactome. Weimann M, et al. Nat Methods, 2013 Apr. PMID 23455924

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. This supports the notion that de novo mutations in ZNF480 are extremely rare in schizophrenia
      Title: Investigation of rare variants in LRP1, KPNA1, ALS2CL and ZNF480 genes in schizophrenia patients reflects genetic heterogeneity of the disease.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of zinc finger protein 480 (ZNF480) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • MGC32104

    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
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 480

    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_001297624.2 → NP_001284553.1  zinc finger protein 480 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which lacks an internal segment and is shorter, compared to isoform 1.
      Source sequence(s)
      AC010320, AK303271, AL832560, DA501214
      Consensus CDS
      CCDS77346.1
      UniProtKB/TrEMBL
      F8WEZ9
      Related
      ENSP00000334164.6, ENST00000334564.11
      Conserved Domains (6) summary
      smart00349
      Location:27 → 67
      KRAB; krueppel associated box
      COG5048
      Location:115 → 458
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:302 → 322
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:356 → 378
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:27 → 66
      KRAB; KRAB box
      pfam13465
      Location:454 → 479
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001297625.2 → NP_001284554.1  zinc finger protein 480 isoform 3

      See identical proteins and their annotated locations for NP_001284554.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 3, which has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC010320, AK096442, AL832560, DA501214
      Consensus CDS
      CCDS74437.1
      UniProtKB/Swiss-Prot
      Q8WV37
      Related
      ENSP00000335670.6, ENST00000335090.6
      Conserved Domains (4) summary
      COG5048
      Location:81 → 424
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:268 → 288
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:322 → 344
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:420 → 445
      zf-H2C2_2; Zinc-finger double domain

    3. NM_001412109.1 → NP_001399038.1  zinc finger protein 480 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) represents an alternate allele of this gene in several human genome assemblies including T2T-CHM13v2.0. It includes a 'TG' deletion (rs3217319) compared to GRCh38, resulting in the use of a downstream start codon. The encoded protein (isoform 4) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      CP068259

    4. NM_144684.4 → NP_653285.2  zinc finger protein 480 isoform 1

      See identical proteins and their annotated locations for NP_653285.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein.
      Source sequence(s)
      AC010320, AK096442, AK303271, AL832560, AY512662, DA501214
      Consensus CDS
      CCDS12850.2
      UniProtKB/Swiss-Prot
      Q5JPG9, Q6P0Q4, Q8N1M5, Q8WV37
      Related
      ENSP00000471754.1, ENST00000595962.6
      Conserved Domains (6) summary
      smart00349
      Location:27 → 87
      KRAB; krueppel associated box
      COG5048
      Location:158 → 501
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:345 → 365
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:399 → 421
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:27 → 66
      KRAB; KRAB box
      pfam13465
      Location:497 → 522
      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
      52297169..52325922
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      55384358..55413117
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WV37.2 GenPept UniProtKB/Swiss-Prot:Q8WV37

    Gene LinkOut

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

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