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

    Gene ID: 147658, updated on 10-Dec-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, Dec 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    all
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    Genomic context

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    See ZNF534 in Genome Data Viewer
    Location:
    19q13.41
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (52429148..52452263)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (55513831..55536813)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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)

    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_2024_08

    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

    Gene LinkOut

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

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