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ZNF554 zinc finger protein 554 [ Homo sapiens (human) ]

Gene ID: 115196, updated on 5-Mar-2024

Summary

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Official Symbol
ZNF554provided by HGNC
Official Full Name
zinc finger protein 554provided by HGNC
Primary source
HGNC:HGNC:26629
See related
Ensembl:ENSG00000172006 AllianceGenome:HGNC:26629
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 repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 1.5), placenta (RPKM 1.4) and 25 other tissues See more
Orthologs
all
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Genomic context

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Location:
19p13.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (2819868..2836735)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (2795155..2812024)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (2819866..2836733)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2768763-2769263 Neighboring gene small glutamine rich tetratricopeptide repeat co-chaperone alpha Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13718 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13719 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9809 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2786765-2787291 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2787292-2787818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2796022-2796522 Neighboring gene thimet oligopeptidase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2820277-2820970 Neighboring gene MPRA-validated peak3238 silencer Neighboring gene MPRA-validated peak3239 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9814 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9815 Neighboring gene zinc finger protein 555 Neighboring gene zinc finger protein 556 Neighboring gene ribosomal protein L35a pseudogene 38

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. Decreased Expression of ZNF554 in Gliomas is Associated with the Activation of Tumor Pathways and Shorter Patient Survival. Balogh A, et al. Int J Mol Sci, 2020 Aug 11. PMID 32796700, Free PMC Article
  2. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Dias Neto E, et al. Proc Natl Acad Sci U S A, 2000 Mar 28. PMID 10737800, 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. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Bennett EJ, et al. Cell, 2010 Dec 10. PMID 21145461, Free PMC Article
  5. OpenCell: Endogenous tagging for the cartography of human cellular organization. Cho NH, et al. Science, 2022 Mar 11. PMID 35271311, Free PMC Article

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Dysfunction of ZNF554 promotes ROS-induced apoptosis and autophagy in Fetal Growth Restriction via the p62-Keap1-Nrf2 pathway.
    Title: Dysfunction of ZNF554 promotes ROS-induced apoptosis and autophagy in Fetal Growth Restriction via the p62-Keap1-Nrf2 pathway.
  2. Decreased Expression of ZNF554 in Gliomas is Associated with the Activation of Tumor Pathways and Shorter Patient Survival.
    Title: Decreased Expression of ZNF554 in Gliomas is Associated with the Activation of Tumor Pathways and Shorter Patient Survival.
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

  • FLJ34817

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 transcription 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
located_in nucleolus 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
  

General protein information

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Preferred Names
zinc finger protein 554

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_001102651.2 → NP_001096121.1  zinc finger protein 554

    See identical proteins and their annotated locations for NP_001096121.1

    Status: VALIDATED

    Source sequence(s)
    AC006130, AC006538, AK027860, AK092136, BC000113, BF772510, DC319914
    Consensus CDS
    CCDS42462.1
    UniProtKB/Swiss-Prot
    Q86TJ5, Q8NAT3, Q9BWN3
    Related
    ENSP00000321132.4, ENST00000317243.10
    Conserved Domains (4) summary
    COG5048
    Location:350 → 532
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:382 → 402
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:324 → 346
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:44 → 84
    KRAB; KRAB box

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
    2819868..2836735
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017026235.2 → XP_016881724.1  zinc finger protein 554 isoform X3

    Conserved Domains (4) summary
    COG5048
    Location:200 → 382
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:232 → 252
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:174 → 196
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:328 → 353
    zf-H2C2_2; Zinc-finger double domain

  2. XM_047438128.1 → XP_047294084.1  zinc finger protein 554 isoform X2

  3. XM_017026234.2 → XP_016881723.1  zinc finger protein 554 isoform X1

  4. XM_011527667.4 → XP_011525969.1  zinc finger protein 554 isoform X4

    Conserved Domains (2) summary
    smart00349
    Location:45 → 89
    KRAB; krueppel associated box
    pfam01352
    Location:45 → 84
    KRAB; KRAB box

  5. XM_006722635.4 → XP_006722698.1  zinc finger protein 554 isoform X3

    See identical proteins and their annotated locations for XP_006722698.1

    Conserved Domains (4) summary
    COG5048
    Location:200 → 382
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:232 → 252
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:174 → 196
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:328 → 353
    zf-H2C2_2; Zinc-finger double domain

  6. XM_017026236.2 → XP_016881725.1  zinc finger protein 554 isoform X3

    Conserved Domains (4) summary
    COG5048
    Location:200 → 382
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:232 → 252
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:174 → 196
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:328 → 353
    zf-H2C2_2; Zinc-finger double domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    2795155..2812024
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319710.1 → XP_054175685.1  zinc finger protein 554 isoform X3

  2. XM_054319709.1 → XP_054175684.1  zinc finger protein 554 isoform X2

  3. XM_054319708.1 → XP_054175683.1  zinc finger protein 554 isoform X1

  4. XM_054319713.1 → XP_054175688.1  zinc finger protein 554 isoform X4

  5. XM_054319712.1 → XP_054175687.1  zinc finger protein 554 isoform X3

  6. XM_054319711.1 → XP_054175686.1  zinc finger protein 554 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_152303.2: Suppressed sequence

    Description
    NM_152303.2: This RefSeq was permanently suppressed because it contains the wrong CDS, and the correct CDS makes it a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86TJ5.1 GenPept UniProtKB/Swiss-Prot:Q86TJ5

Gene LinkOut

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