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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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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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