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ZFR zinc finger RNA binding protein [ Homo sapiens (human) ]

Gene ID: 51663, updated on 11-Apr-2024

Summary

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Official Symbol
ZFRprovided by HGNC
Official Full Name
zinc finger RNA binding proteinprovided by HGNC
Primary source
HGNC:HGNC:17277
See related
Ensembl:ENSG00000056097 MIM:615635; AllianceGenome:HGNC:17277
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ZFR1; SPG71
Summary
This gene encodes an RNA-binding protein characterized by its DZF (domain associated with zinc fingers) domain. The encoded protein may play a role in the nucleocytoplasmic shuttling of another RNA-binding protein, Staufen homolog 2, in neurons. Expression of this gene is regulated through alternative polyadenylation that mediates differential microRNA targeting. Elevated expression of this gene has been observed in human patients with pancreatic cancer and knockdown of this gene may result in reduced viability and invasion of pancreatic cancer cells. [provided by RefSeq, Sep 2016]
Expression
Ubiquitous expression in brain (RPKM 34.3), testis (RPKM 25.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
5p13.3
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (32354350..32444740, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (32468061..32558413, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (32354456..32444846, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1079, pseudogene Neighboring gene myotubularin related protein 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22441 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22443 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:32310088-32310248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22444 Neighboring gene RNA, U6 small nuclear 378, pseudogene Neighboring gene MPRA-validated peak5220 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr5:32372846-32373049 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:32376171-32376388 Neighboring gene microRNA 579 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:32443940-32444497 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15958 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:32501369-32502015 Neighboring gene uncharacterized LOC124900954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:32511632-32512132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22446 Neighboring gene TMEM183A pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22451 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:32576632-32576802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15959 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15960 Neighboring gene SUB1 regulator of transcription

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. O- glycosylation can regulate the proliferation and migration of human retinal microvascular endothelial cells through ZFR in high glucose condition. Xing X, et al. Biochem Biophys Res Commun, 2019 May 7. PMID 30914198
  2. Knockdown of ZFR suppresses cell proliferation and invasion of human pancreatic cancer. Zhao X, et al. Biol Res, 2016 May 13. PMID 27177590, Free PMC Article
  3. The circular RNA circZFR phosphorylates Rb promoting cervical cancer progression by regulating the SSBP1/CDK2/cyclin E1 complex. Zhou M, et al. J Exp Clin Cancer Res, 2021 Jan 30. PMID 33516252, Free PMC Article
  4. ZFR promotes cell proliferation and tumor development in colorectal and liver cancers. Long Y, et al. Biochem Biophys Res Commun, 2019 Jun 11. PMID 31010678
  5. MiR-141-3p functions as a tumor suppressor through directly targeting ZFR in non-small cell lung cancer. Li W, et al. Biochem Biophys Res Commun, 2019 Feb 12. PMID 30611568

See all (134) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Circulating RNA ZFR promotes hepatocellular carcinoma cell proliferation and epithelial-mesenchymal transition process through miR-624-3p/WEE1 axis.
    Title: Circulating RNA ZFR promotes hepatocellular carcinoma cell proliferation and epithelial-mesenchymal transition process through miR-624-3p/WEE1 axis.
  2. Circular RNA circZFR Promotes Hepatocellular Carcinoma Progression by Regulating miR-375/HMGA2 Axis.
    Title: Circular RNA circZFR Promotes Hepatocellular Carcinoma Progression by Regulating miR-375/HMGA2 Axis.
  3. The circular RNA circZFR phosphorylates Rb promoting cervical cancer progression by regulating the SSBP1/CDK2/cyclin E1 complex.
    Title: The circular RNA circZFR phosphorylates Rb promoting cervical cancer progression by regulating the SSBP1/CDK2/cyclin E1 complex.
  4. overexpression of ZFR in CRC and liver cancer cells led to accelerated tumor development. Consistently, knockdown of ZFR resulted in significantly decelerated tumor development.
    Title: ZFR promotes cell proliferation and tumor development in colorectal and liver cancers.
  5. Hyperglycaemia elevates ZFR in vivo and in vitro. ZFR can promote the proliferation and migration of human retinal microvascular endothelial cells cultured in high glucose condition.
    Title: O- glycosylation can regulate the proliferation and migration of human retinal microvascular endothelial cells through ZFR in high glucose condition.
  6. ZFR was confirmed as a target gene of miR-141-3p and negatively correlated with miR-141-3p expression in non-small cell lung cancer tissues.
    Title: MiR-141-3p functions as a tumor suppressor through directly targeting ZFR in non-small cell lung cancer.
  7. ZFR expression is tightly controlled during macrophage development; monocytes express truncated ZFR isoforms, while macrophages induce full-length ZFR to modulate macrophage-specific alternative splicing.
    Title: ZFR coordinates crosstalk between RNA decay and transcription in innate immunity.
  8. Identified a new circRNA, circZFR, that was significantly upregulated in papillary thyroid carcinoma (PTC). CircZFR could promote C8orf4 expression via serving as a competing endogenous RNA of miR-1261 in PTC cells. Rescue assays indicated that restoration of C8orf4 significantly attenuated the inhibitory effects of circZFR knockdown on PTC cell proliferation, migration and invasion.
    Title: Circular RNA circZFR contributes to papillary thyroid cancer cell proliferation and invasion by sponging miR-1261 and facilitating C8orf4 expression.
  9. polyadenylation allows differential negative feedback of human miRNA miR-579 on its host gene ZFR
    Title: Alternative polyadenylation allows differential negative feedback of human miRNA miR-579 on its host gene ZFR.
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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify zinc finger RNA binding protein (ZFR), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify zinc finger RNA binding protein (ZFR), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify zinc finger RNA binding protein (ZFR), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify zinc finger RNA binding protein (ZFR), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ41312

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding HDA PubMed 
enables double-stranded RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables single-stranded RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
zinc finger RNA-binding protein
Names
M-phase phosphoprotein homolog

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_051591.1 RefSeqGene

    Range
    5022..95412
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_016107.5 → NP_057191.2  zinc finger RNA-binding protein

    See identical proteins and their annotated locations for NP_057191.2

    Status: REVIEWED

    Source sequence(s)
    AJ314790, AL137258, BC017879, BC030540, BC051893, DA691446
    Consensus CDS
    CCDS34139.1
    UniProtKB/Swiss-Prot
    B2RNR5, Q05C08, Q3B7X5, Q6P5A3, Q86UA0, Q96KR1, Q9H6V4, Q9NTI1, Q9Y687
    UniProtKB/TrEMBL
    B2RNR6
    Related
    ENSP00000265069.8, ENST00000265069.13
    Conserved Domains (4) summary
    smart00572
    Location:784 → 1038
    DZF; domain in DSRM or ZnF_C2H2 domain containing proteins
    smart00451
    Location:581 → 612
    ZnF_U1; U1-like zinc finger
    sd00020
    Location:584 → 606
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam05647
    Location:420 → 477
    Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like

RNA

  1. NR_144318.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC008949

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    32354350..32444740 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    32468061..32558413 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96KR1.2 GenPept UniProtKB/Swiss-Prot:Q96KR1

Gene LinkOut

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