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    ZNF500 zinc finger protein 500 [ Homo sapiens (human) ]

    Gene ID: 26048, updated on 5-Mar-2024

    Summary

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    Official Symbol
    ZNF500provided by HGNC
    Official Full Name
    zinc finger protein 500provided by HGNC
    Primary source
    HGNC:HGNC:23716
    See related
    Ensembl:ENSG00000103199 AllianceGenome:HGNC:23716
    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
    ZSCAN50; ZKSCAN18
    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, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 3.6), spleen (RPKM 2.4) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ZNF500 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (4744245..4767162, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (4774468..4796609, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (4798240..4817163, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene hESC enhancers GRCh37_chr16:4743475-4743982 and GRCh37_chr16:4743983-4744490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4745093-4745593 Neighboring gene nudix hydrolase 16 like 1 Neighboring gene ankyrin repeat and sterile alpha motif domain containing 3 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr16:4763641-4764282 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr16:4764283-4764922 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr16:4768049-4768651 and GRCh37_chr16:4768652-4769253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7164 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7163 Neighboring gene dynein axonemal assembly factor 8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10344 Neighboring gene septin 12 Neighboring gene small integral membrane protein 22 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:4852142-4852642 Neighboring gene rogdi atypical leucine zipper

    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. Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. Nagase T, et al. DNA Res, 1998 Feb 28. PMID 9628581
    2. Generation and analysis of 280,000 human expressed sequence tags. Hillier LD, et al. Genome Res, 1996 Sep. PMID 8889549
    3. Large-scale concatenation cDNA sequencing. Yu W, et al. Genome Res, 1997 Apr. PMID 9110174, Free PMC Article
    4. A "double adaptor" method for improved shotgun library construction. Andersson B, et al. Anal Biochem, 1996 Apr 5. PMID 8619474
    5. Sequential genome-wide CRISPR-Cas9 screens identify genes regulating cell-surface expression of tetraspanins. Yang J, et al. Cell Rep, 2023 Feb 28. PMID 36724073

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ZNF500 abolishes breast cancer proliferation and sensitizes chemotherapy by stabilizing P53 via competing with MDM2.
      Title: ZNF500 abolishes breast cancer proliferation and sensitizes chemotherapy by stabilizing P53 via competing with MDM2.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 500
    Names
    zinc finger protein with KRAB and SCAN domains 18

    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_001303450.2 → NP_001290379.1  zinc finger protein 500 isoform 2

      See identical proteins and their annotated locations for NP_001290379.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate segment in the 3' coding region compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AB011129, AC020663, AK297993
      Consensus CDS
      CCDS76814.1
      UniProtKB/Swiss-Prot
      O60304
      Related
      ENSP00000445714.1, ENST00000545009.1
      Conserved Domains (7) summary
      smart00431
      Location:46 → 151
      SCAN; leucine rich region
      cd07765
      Location:224 → 247
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      COG5048
      Location:321 → 380
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:327 → 347
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:325 → 347
      zf-C2H2; Zinc finger, C2H2 type
      pfam02023
      Location:46 → 134
      SCAN; SCAN domain
      pfam13465
      Location:367 → 392
      zf-H2C2_2; Zinc-finger double domain

    2. NM_021646.4 → NP_067678.1  zinc finger protein 500 isoform 1

      See identical proteins and their annotated locations for NP_067678.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB011129, AC020663, AK291792, BM678198
      Consensus CDS
      CCDS32383.1
      UniProtKB/Swiss-Prot
      A8K6X7, B4DNN9, O60304, Q0VAL2, Q96CQ8, Q9BTG0
      Related
      ENSP00000219478.5, ENST00000219478.11
      Conserved Domains (7) summary
      smart00431
      Location:46 → 151
      SCAN; leucine rich region
      cd07765
      Location:224 → 247
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      COG5048
      Location:320 → 459
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:327 → 347
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:325 → 347
      zf-C2H2; Zinc finger, C2H2 type
      pfam02023
      Location:46 → 134
      SCAN; SCAN domain
      pfam13465
      Location:367 → 392
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      4744245..4767162 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011522453.3 → XP_011520755.1  zinc finger protein 500 isoform X1

      Conserved Domains (7) summary
      smart00431
      Location:46 → 151
      SCAN; leucine rich region
      cd07765
      Location:224 → 247
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      COG5048
      Location:363 → 437
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:327 → 347
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:325 → 347
      zf-C2H2; Zinc finger, C2H2 type
      pfam02023
      Location:46 → 134
      SCAN; SCAN domain
      pfam13465
      Location:367 → 392
      zf-H2C2_2; Zinc-finger double domain

    2. XM_005255243.5 → XP_005255300.1  zinc finger protein 500 isoform X2

      Conserved Domains (5) summary
      cd07765
      Location:107 → 130
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      COG5048
      Location:203 → 342
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:210 → 230
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:208 → 230
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:250 → 275
      zf-H2C2_2; Zinc-finger double domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      4774468..4796609 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054380017.1 → XP_054235992.1  zinc finger protein 500 isoform X1

    2. XM_054380019.1 → XP_054235994.1  zinc finger protein 500 isoform X3

      UniProtKB/TrEMBL
      Q0VAL1

    3. XM_054380018.1 → XP_054235993.1  zinc finger protein 500 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O60304.2 GenPept UniProtKB/Swiss-Prot:O60304

    Gene LinkOut

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