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    ZNF496 zinc finger protein 496 [ Homo sapiens (human) ]

    Gene ID: 84838, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ZNF496provided by HGNC
    Official Full Name
    zinc finger protein 496provided by HGNC
    Primary source
    HGNC:HGNC:23713
    See related
    Ensembl:ENSG00000162714 MIM:613911; AllianceGenome:HGNC:23713
    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
    Also known as
    NIZP1; ZFP496; ZSCAN49; ZKSCAN17
    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 positive regulation of DNA-templated transcription and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 3.4), ovary (RPKM 3.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZNF496 in Genome Data Viewer
    Location:
    1q44
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (247297415..247331867, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (246730535..246764981, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (247460717..247495169, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene vomeronasal 1 receptor 5 (gene/pseudogene) Neighboring gene uncharacterized LOC105373273 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:247453849-247454367 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:247462225-247463124 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:247463125-247464023 Neighboring gene NANOG hESC enhancer GRCh37_chr1:247485935-247486439 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:247492160-247492662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2044 Neighboring gene Sharpr-MPRA regulatory region 5917 Neighboring gene Sharpr-MPRA regulatory region 7964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:247499115-247499615 Neighboring gene uncharacterized LOC124904574 Neighboring gene Sharpr-MPRA regulatory region 1744 Neighboring gene ZNF496 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:247525936-247526480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2047 Neighboring gene uncharacterized LOC107985375 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:247556143-247556425

    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. KRAB-containing zinc finger protein ZNF496 inhibits breast cancer cell proliferation by selectively repressing ERα activity. Wang J, et al. Biochim Biophys Acta Gene Regul Mech, 2018 Jul 20. PMID 30012466
    2. NSD1 PHD domains bind methylated H3K4 and H3K9 using interactions disrupted by point mutations in human sotos syndrome. Pasillas MP, et al. Hum Mutat, 2011 Mar. PMID 21972110
    3. The NIZP1 KRAB and C2HR domains cross-talk for transcriptional regulation. Losson R, et al. Biochim Biophys Acta, 2010 May-Jun. PMID 20176155
    4. Nizp1, a novel multitype zinc finger protein that interacts with the NSD1 histone lysine methyltransferase through a unique C2HR motif. Nielsen AL, et al. Mol Cell Biol, 2004 Jun. PMID 15169884, Free PMC Article
    5. The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification. Helleboid PY, et al. EMBO J, 2019 Sep 16. PMID 31403225, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC15548

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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 positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 496
    Names
    NSD1 (nuclear receptor binding SET-domain containing 1)-interacting zinc finger protein 1
    zinc finger protein with KRAB and SCAN domains 17

    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_001329733.2 → NP_001316662.1  zinc finger protein 496 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC104335
      Conserved Domains (2) summary
      cd07765
      Location:222 → 259
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      pfam02023
      Location:50 → 126
      SCAN; SCAN domain

    2. NM_032752.3 → NP_116141.1  zinc finger protein 496 isoform 1

      See identical proteins and their annotated locations for NP_116141.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC104335, BC007263, BC025794, BU740940, HY023128
      Consensus CDS
      CCDS1631.1
      UniProtKB/Swiss-Prot
      Q8TBS2, Q96IT1
      UniProtKB/TrEMBL
      A0A0C4DGR5
      Related
      ENSP00000507236.1, ENST00000682384.1
      Conserved Domains (6) summary
      cd07765
      Location:222 → 259
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      smart00349
      Location:223 → 275
      KRAB; krueppel associated box
      COG5048
      Location:427 → 586
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:408 → 428
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:463 → 485
      zf-C2H2; Zinc finger, C2H2 type
      pfam02023
      Location:50 → 126
      SCAN; SCAN 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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      247297415..247331867 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791757.1 Reference GRCh38.p14 PATCHES

      Range
      63858..98310 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      246730535..246764981 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96IT1.1 GenPept UniProtKB/Swiss-Prot:Q96IT1

    Gene LinkOut

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

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