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ZNF540 zinc finger protein 540 [ Homo sapiens (human) ]

Gene ID: 163255, updated on 7-Apr-2024

Summary

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Official Symbol
ZNF540provided by HGNC
Official Full Name
zinc finger protein 540provided by HGNC
Primary source
HGNC:HGNC:25331
See related
Ensembl:ENSG00000171817 MIM:613903; AllianceGenome:HGNC:25331
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
Nbla10512
Summary
Enables translation repressor activity, mRNA regulatory element binding. Involved in negative regulation of transcription, DNA-templated and negative regulation of translation. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 3.9), thyroid (RPKM 3.7) and 23 other tissues See more
Orthologs
all
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Genomic context

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Location:
19q13.12
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (37551374..37614179)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (40353192..40415937)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (38042276..38105080)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ZNF793 antisense RNA 1 (head to head) Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:37996759-37997550 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:37997551-37998342 Neighboring gene zinc finger protein 793 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:38020876-38021698 Neighboring gene uncharacterized LOC124904708 Neighboring gene ZNF571 antisense RNA 1 Neighboring gene zinc finger protein 571 Neighboring gene MT-ND4 pseudogene 41 Neighboring gene MT-ND5 pseudogene 45 Neighboring gene MT-CO1 pseudogene 41 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38084654-38085335 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38085336-38086018 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14554 Neighboring gene ZFP30 zinc finger protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10556 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38146535-38147522 Neighboring gene zinc finger protein 781

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. A novel human zinc finger protein ZNF540 interacts with MVP and inhibits transcriptional activities of the ERK signal pathway. Xiang Z, et al. Biochem Biophys Res Commun, 2006 Aug 18. PMID 16815308
  2. 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
  3. 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
  4. Toward a confocal subcellular atlas of the human proteome. Barbe L, et al. Mol Cell Proteomics, 2008 Mar. PMID 18029348
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Taken together, these results suggest that ZNF540 may act as a transcriptional repressor in MAPK signaling pathway to mediate cellular functions.
    Title: A novel human zinc finger protein ZNF540 interacts with MVP and inhibits transcriptional activities of the ERK signal pathway.
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

Clone Names

  • FLJ16004, DKFZp313K2238, DKFZp547B0714

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 mRNA regulatory element binding translation repressor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of translation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in intracellular membrane-bounded organelle 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
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
zinc finger protein 540
Names
CTD-3064H18.6
putative protein product of Nbla10512

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_001172225.3 → NP_001165696.1  zinc finger protein 540 isoform a

    See identical proteins and their annotated locations for NP_001165696.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform a. Both variants 1 and 2 encode the same isoform (a), which is longer than isoform b.
    Source sequence(s)
    AL832315, BC017940, BE464266
    UniProtKB/Swiss-Prot
    A0AVS5, A8K371, Q05D58, Q3LIC5, Q6ZN36, Q7Z3C8, Q86T31, Q8NDQ6
    Related
    ENSP00000324598.3, ENST00000316433.9
    Conserved Domains (4) summary
    smart00349
    Location:6 → 66
    KRAB; krueppel associated box
    COG5048
    Location:241 → 620
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:581 → 601
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:621 → 646
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001172226.3 → NP_001165697.1  zinc finger protein 540 isoform b

    See identical proteins and their annotated locations for NP_001165697.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the coding region, compared to variant 1. The resulting isoform (b) lacks an internal segment, compared to isoform a.
    Source sequence(s)
    AL832100, AL832315, BC017940, BE464266
    Consensus CDS
    CCDS54258.1
    UniProtKB/Swiss-Prot
    Q8NDQ6
    Related
    ENSP00000467118.1, ENST00000589117.5
    Conserved Domains (5) summary
    smart00349
    Location:6 → 47
    KRAB; krueppel associated box
    COG5048
    Location:209 → 614
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:549 → 569
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:6 → 45
    KRAB; KRAB box
    pfam13465
    Location:561 → 584
    zf-H2C2_2; Zinc-finger double domain

  3. NM_152606.5 → NP_689819.1  zinc finger protein 540 isoform a

    See identical proteins and their annotated locations for NP_689819.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate 5' UTR exon compared to variant 1, and represents a read-through transcript between the upstream non-coding LOC100507433 locus (GeneID 100507433) and the downstream ZNF540 locus (GeneID 163255).Both variants 1 and 2 encode the same isoform (a), which is longer than isoform b.
    Source sequence(s)
    AC022148, AL832315, BE464266
    UniProtKB/Swiss-Prot
    A0AVS5, A8K371, Q05D58, Q3LIC5, Q6ZN36, Q7Z3C8, Q86T31, Q8NDQ6
    Related
    ENSP00000466274.1, ENST00000592533.5
    Conserved Domains (4) summary
    smart00349
    Location:6 → 66
    KRAB; krueppel associated box
    COG5048
    Location:241 → 620
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:581 → 601
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:621 → 646
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    37551374..37614179
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    40353192..40415937
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NDQ6.1 GenPept UniProtKB/Swiss-Prot:Q8NDQ6

Gene LinkOut

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

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