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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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    See ZNF540 in Genome Data Viewer
    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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