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ZNF562 zinc finger protein 562 [ Homo sapiens (human) ]

Gene ID: 54811, updated on 5-Mar-2024

Summary

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Official Symbol
ZNF562provided by HGNC
Official Full Name
zinc finger protein 562provided by HGNC
Primary source
HGNC:HGNC:25950
See related
Ensembl:ENSG00000171466 AllianceGenome:HGNC:25950
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
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, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in esophagus (RPKM 4.1), urinary bladder (RPKM 3.4) and 25 other tissues See more
Orthologs
all
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Genomic context

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Location:
19p13.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (9641807..9675100, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (9768019..9801288, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (9752483..9785776, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 561 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:9731087-9731669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13932 Neighboring gene ZNF561 antisense RNA 1 (head to head) Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:9784745-9785944 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:9785983-9786982 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:9791103-9791685 Neighboring gene ribosomal protein S4X pseudogene 22 Neighboring gene zinc finger protein 812, pseudogene

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. Gene expression profile of human bone marrow stromal cells: high-throughput expressed sequence tag sequencing analysis. Jia L, et al. Genomics, 2002 Jan. PMID 11827452
  2. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. Suzuki Y, et al. Genome Res, 2004 Sep. PMID 15342556, Free PMC Article
  3. Ubiquitin-mediated proteolysis of HuR by heat shock. Abdelmohsen K, et al. EMBO J, 2009 May 6. PMID 19322201, Free PMC Article
  4. Cullin 3 Exon 9 Deletion in Familial Hyperkalemic Hypertension Impairs Cullin3-Ring-E3 Ligase (CRL3) Dynamic Regulation and Cycling. Kouranti I, et al. Int J Mol Sci, 2022 May 5. PMID 35563538, Free PMC Article
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
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

  • FLJ20079, MGC126160

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 DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
zinc finger protein 562

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_001130031.2 → NP_001123503.1  zinc finger protein 562 isoform a

    See identical proteins and their annotated locations for NP_001123503.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer protein (isoform a). Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC008759, AI753280, BP221824, DC405554
    Consensus CDS
    CCDS45956.1
    UniProtKB/Swiss-Prot
    Q32MN2, Q6V9R5, Q9NXS5
    Related
    ENSP00000410734.1, ENST00000453372.7
    Conserved Domains (4) summary
    COG5048
    Location:258 → 420
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:318 → 338
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:181 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:40 → 81
    KRAB; KRAB box

  2. NM_001130032.2 → NP_001123504.1  zinc finger protein 562 isoform a

    See identical proteins and their annotated locations for NP_001123504.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses a different splice site in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC008759, AI753280, BP221824, DC403290
    Consensus CDS
    CCDS45956.1
    UniProtKB/Swiss-Prot
    Q32MN2, Q6V9R5, Q9NXS5
    Conserved Domains (4) summary
    COG5048
    Location:258 → 420
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:318 → 338
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:181 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:40 → 81
    KRAB; KRAB box

  3. NM_001300885.2 → NP_001287814.1  zinc finger protein 562 isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform c, which is shorter by an amino acid, compared to isoform a.
    Source sequence(s)
    AC008759, AI753280, AK297446, AK304370, BC109062
    Consensus CDS
    CCDS74280.1
    UniProtKB/TrEMBL
    K7EIE6
    Related
    ENSP00000464716.1, ENST00000590155.5
    Conserved Domains (7) summary
    smart00349
    Location:41 → 85
    KRAB; krueppel associated box
    COG5048
    Location:257 → 419
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:317 → 337
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:180 → 197
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:287 → 309
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:41 → 80
    KRAB; KRAB box
    pfam13465
    Location:358 → 382
    zf-H2C2_2; Zinc-finger double domain

  4. NM_017656.4 → NP_060126.2  zinc finger protein 562 isoform b

    See identical proteins and their annotated locations for NP_060126.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks alternate segments in the 5' coding region, compared to variant 1. The resulting protein (isoform b) has a shorter N-terminus when it is compared to isoform a.
    Source sequence(s)
    AC008759, AI753280, AK000086, BP221824
    Consensus CDS
    CCDS12217.1
    UniProtKB/Swiss-Prot
    Q6V9R5
    Related
    ENSP00000293648.3, ENST00000293648.8
    Conserved Domains (3) summary
    COG5048
    Location:186 → 348
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:246 → 266
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:287 → 311
    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
    9641807..9675100 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047438996.1 → XP_047294952.1  zinc finger protein 562 isoform X3

  2. XM_047438995.1 → XP_047294951.1  zinc finger protein 562 isoform X2

  3. XM_017026898.3 → XP_016882387.1  zinc finger protein 562 isoform X1

    UniProtKB/TrEMBL
    K7EIE6
    Conserved Domains (7) summary
    smart00349
    Location:41 → 85
    KRAB; krueppel associated box
    COG5048
    Location:257 → 419
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:317 → 337
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:180 → 197
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:287 → 309
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:41 → 80
    KRAB; KRAB box
    pfam13465
    Location:358 → 382
    zf-H2C2_2; Zinc-finger double domain

  4. XM_047438994.1 → XP_047294950.1  zinc finger protein 562 isoform X1

    UniProtKB/TrEMBL
    K7EIE6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    9768019..9801288 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054321307.1 → XP_054177282.1  zinc finger protein 562 isoform X3

  2. XM_054321306.1 → XP_054177281.1  zinc finger protein 562 isoform X2

  3. XM_054321304.1 → XP_054177279.1  zinc finger protein 562 isoform X1

    UniProtKB/TrEMBL
    K7EIE6

  4. XM_054321305.1 → XP_054177280.1  zinc finger protein 562 isoform X1

    UniProtKB/TrEMBL
    K7EIE6
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6V9R5.2 GenPept UniProtKB/Swiss-Prot:Q6V9R5

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