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ZNF546 zinc finger protein 546 [ Homo sapiens (human) ]

Gene ID: 339327, updated on 5-Mar-2024

Summary

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Official Symbol
ZNF546provided by HGNC
Official Full Name
zinc finger protein 546provided by HGNC
Primary source
HGNC:HGNC:28671
See related
Ensembl:ENSG00000187187 AllianceGenome:HGNC:28671
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
ZNF49
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 integral component of membrane. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 3.3), thyroid (RPKM 0.9) and 22 other tissues See more
Orthologs
all
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Genomic context

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Location:
19q13.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (39997060..40021038)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (42817266..42841244)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (40502967..40526945)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14634 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14635 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:40477356-40478035 Neighboring gene proteasome 26S subunit, ATPase 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:40502115-40502616 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:40502617-40503116 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10615 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:40520495-40521694 Neighboring gene PAT1 homolog 1, processing body mRNA decay factor pseudogene Neighboring gene zinc finger protein 780B Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:40541448-40542647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14637

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. Clustering of C2-H2 zinc finger motif sequences within telomeric and fragile site regions of human chromosomes. Lichter P, et al. Genomics, 1992 Aug. PMID 1505991
  2. A germline-specific class of small RNAs binds mammalian Piwi proteins. Girard A, et al. Nature, 2006 Jul 13. PMID 16751776
  3. BAP1 regulation of the key adaptor protein NCoR1 is critical for γ-globin gene repression. Yu L, et al. Genes Dev, 2018 Dec 1. PMID 30463901, Free PMC Article
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  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

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

  • MGC43537

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
  
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 546
Names
CTC-471F3.6
zinc finger protein 49

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_001297763.2 → NP_001284692.1  zinc finger protein 546 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001284692.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    AC007842, AF087985, AK122968, AK292528, DA217689
    Consensus CDS
    CCDS77297.1
    UniProtKB/TrEMBL
    M0QY24
    Related
    ENSP00000469540.1, ENST00000600094.5
    Conserved Domains (5) summary
    smart00349
    Location:34 → 94
    KRAB; krueppel associated box
    COG5048
    Location:357 → 797
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:557 → 577
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:34 → 73
    KRAB; KRAB box
    pfam13465
    Location:625 → 650
    zf-H2C2_2; Zinc-finger double domain

  2. NM_178544.5 → NP_848639.2  zinc finger protein 546 isoform 1

    See identical proteins and their annotated locations for NP_848639.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC007842, AF087985, AK122968, AK292528, DA217689
    Consensus CDS
    CCDS12548.1
    UniProtKB/Swiss-Prot
    A8K913, Q86UE3
    Related
    ENSP00000339823.3, ENST00000347077.9
    Conserved Domains (5) summary
    smart00349
    Location:60 → 120
    KRAB; krueppel associated box
    COG5048
    Location:383 → 823
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:583 → 603
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:60 → 99
    KRAB; KRAB box
    pfam13465
    Location:651 → 676
    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
    39997060..40021038
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_009646206.1 Reference GRCh38.p14 PATCHES

    Range
    272203..296181
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    42817266..42841244
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86UE3.2 GenPept UniProtKB/Swiss-Prot:Q86UE3

Gene LinkOut

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