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ZNF534 zinc finger protein 534 [ Homo sapiens (human) ]

Gene ID: 147658, updated on 5-Mar-2024

Summary

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Official Symbol
ZNF534provided by HGNC
Official Full Name
zinc finger protein 534provided by HGNC
Primary source
HGNC:HGNC:26337
See related
Ensembl:ENSG00000198633 AllianceGenome:HGNC:26337
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
KRBO3
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. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
all
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Genomic context

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Location:
19q13.41
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (52429148..52452263)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (55513831..55536813)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (52932401..52955516)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:52900414-52901613 Neighboring gene zinc finger protein 528 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:52923769-52924534 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:52924535-52925300 Neighboring gene developmental pluripotency associated 5 pseudogene 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:52956248-52957447 Neighboring gene DUT pseudogene Neighboring gene zinc finger protein 578 Neighboring gene zinc finger protein 347 pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:52986584-52987370 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr19:52987371-52988156 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:52990721-52991690 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:52996369-52997007 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:52997008-52997645 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:53003665-53004504 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:53029540-53030366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:53030367-53031194 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:53039321-53039907 Neighboring gene zinc finger protein 808 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:53061637-53062248 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:53062249-53062862 Neighboring gene ribosomal protein L39 pseudogene 34

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 reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article
  2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

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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Homology

Clone Names

  • FLJ25344

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
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
zinc finger protein 534
Names
KRAB domain only 3
KRAB domain only protein 3

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.

Genomic

  1. NG_054923.1 RefSeqGene

    Range
    5178..18529
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001143938.3 → NP_001137410.1  zinc finger protein 534 isoform 1

    See identical proteins and their annotated locations for NP_001137410.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AB086839, AC010332
    Consensus CDS
    CCDS46166.1
    UniProtKB/Swiss-Prot
    Q76KX8
    Related
    ENSP00000391358.1, ENST00000433050.6
    Conserved Domains (5) summary
    smart00349
    Location:8 → 68
    KRAB; krueppel associated box
    COG5048
    Location:198 → 596
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:524 → 544
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:8 → 47
    KRAB; KRAB box
    pfam13465
    Location:452 → 477
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001143939.3 → NP_001137411.1  zinc finger protein 534 isoform 2

    See identical proteins and their annotated locations for NP_001137411.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region compared to variant 1. Variant 2 represents the longest transcript and encodes the longest isoform (2).
    Source sequence(s)
    AB086840, AC010332
    Consensus CDS
    CCDS46165.1
    UniProtKB/Swiss-Prot
    Q76KX8, Q76KX9
    Related
    ENSP00000327538.6, ENST00000332323.10
    Conserved Domains (5) summary
    smart00349
    Location:8 → 81
    KRAB; krueppel associated box
    COG5048
    Location:211 → 609
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:537 → 557
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:8 → 47
    KRAB; KRAB box
    pfam13465
    Location:465 → 490
    zf-H2C2_2; Zinc-finger double domain

  3. NM_001291368.4 → NP_001278297.1  zinc finger protein 534 isoform 3

    See identical proteins and their annotated locations for NP_001278297.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate 3' exon in the 3' UTR and 3' coding region compared to variant 1. The encoded isoform (3) is shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AB091369, AC010332, AK058073
    Consensus CDS
    CCDS77347.1
    UniProtKB/TrEMBL
    Q1T7F5, Q96LN7
    Related
    ENSP00000301085.4, ENST00000301085.8
    Conserved Domains (2) summary
    smart00349
    Location:8 → 68
    KRAB; krueppel associated box
    pfam01352
    Location:8 → 47
    KRAB; KRAB box

  4. NM_001291369.4 → NP_001278298.1  zinc finger protein 534 isoform 4

    See identical proteins and their annotated locations for NP_001278298.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an exon in the internal coding region and uses an alternate exon in the 3' UTR and 3' coding region, compared to variant 1. The encoded isoform (4) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AB091368, AC010332, AK058073
    Consensus CDS
    CCDS77348.1
    UniProtKB/TrEMBL
    Q1T7F6
    Related
    ENSP00000409421.2, ENST00000432303.6
    Conserved Domains (2) summary
    smart00349
    Location:8 → 49
    KRAB; krueppel associated box
    pfam01352
    Location:8 → 47
    KRAB; KRAB box

  5. NM_001351679.2 → NP_001338608.1  zinc finger protein 534 isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an alternate coding exon compared to variant 1. The resulting isoform (5) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC010332
    Conserved Domains (2) summary
    COG5048
    Location:239 → 633
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:496 → 516
    ZF_C2H2; C2H2 Zn finger [structural motif]

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
    52429148..52452263
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    55513831..55536813
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_182512.1: Suppressed sequence

    Description
    NM_182512.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q76KX8.1 GenPept UniProtKB/Swiss-Prot:Q76KX8

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