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ZNF398 zinc finger protein 398 [ Homo sapiens (human) ]

Gene ID: 57541, updated on 5-Mar-2024

Summary

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Official Symbol
ZNF398provided by HGNC
Official Full Name
zinc finger protein 398provided by HGNC
Primary source
HGNC:HGNC:18373
See related
Ensembl:ENSG00000197024 MIM:618593; AllianceGenome:HGNC:18373
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
P51; P71; ZER6
Summary
This gene encodes a member of the Kruppel family of C2H2-type zinc-finger transcription factor proteins. The encoded protein acts as a transcriptional activator. Two transcript variants encoding distinct isoforms have been identified for this gene. Other transcript variants have been described, but their full length sequence has not been determined. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 4.5), esophagus (RPKM 2.9) and 25 other tissues See more
Orthologs
all
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Genomic context

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See ZNF398 in Genome Data Viewer
Location:
7q36.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (149126408..149183042)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (150308211..150364850)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (148823500..148880134)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148768421-148769413 Neighboring gene zinc finger protein 786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18745 Neighboring gene MPRA-validated peak6836 silencer Neighboring gene MPRA-validated peak6837 silencer Neighboring gene zinc finger protein 425 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:148821330-148821830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:148821831-148822331 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148822579-148823130 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148823131-148823682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26808 Neighboring gene RNA, 7SL, cytoplasmic 521, pseudogene Neighboring gene uncharacterized LOC107986856 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:148842175-148842748 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148842749-148843322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148843323-148843896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26809 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:148844471-148845044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148853225-148853792 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148853793-148854358 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148854359-148854926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26811 Neighboring gene centrosomal protein 83kDa pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr7:148892414-148892735 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26812 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:148900065-148900565 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:148906433-148907147 Neighboring gene zinc finger protein 282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:148916930-148917919 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:148923698-148923905 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:148930294-148931493 Neighboring gene Sharpr-MPRA regulatory region 80 Neighboring gene zinc finger protein 212

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. The transcriptional regulator ZNF398 mediates pluripotency and epithelial character downstream of TGF-beta in human PSCs. Zorzan I, et al. Nat Commun, 2020 May 12. PMID 32398665, Free PMC Article
  2. A novel zinc finger transcription factor with two isoforms that are differentially repressed by estrogen receptor-alpha. Conroy AT, et al. J Biol Chem, 2002 Mar 15. PMID 11779858
  3. p52-ZER6: a determinant of tumor cell sensitivity to MDM2-p53 binding inhibitors. Li WF, et al. Acta Pharmacol Sin, 2023 Mar. PMID 35995868, Free PMC Article
  4. Zinc-finger protein p52-ZER6 accelerates colorectal cancer cell proliferation and tumour progression through promoting p53 ubiquitination. Huang C, et al. EBioMedicine, 2019 Oct. PMID 31521611, Free PMC Article
  5. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Feb 28. PMID 10718198

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The transcriptional regulator ZNF398 mediates pluripotency and epithelial character downstream of TGF-beta in human PSCs.
    Title: The transcriptional regulator ZNF398 mediates pluripotency and epithelial character downstream of TGF-beta in human PSCs.
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

  • KIAA1339

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 positive regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
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
  
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
zinc finger protein 398
Names
zinc finger DNA binding protein ZER6
zinc finger DNA binding protein p52/p71
zinc finger-estrogen receptor interaction, clone 6

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_020781.4 → NP_065832.1  zinc finger protein 398 isoform b

    See identical proteins and their annotated locations for NP_065832.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as p52-ZER6, contains an additional segment in the coding region compared to variant 1. The resulting isoform (b) has a shorter N-terminal, compared to isoform a. Transcription of transcript variant 2 is repressed by estrogen receptor alpha.
    Source sequence(s)
    AC004890, AC073422, AY049743
    Consensus CDS
    CCDS47739.1
    UniProtKB/TrEMBL
    A0A090N8F2
    Related
    ENSP00000389972.2, ENST00000426851.6
    Conserved Domains (4) summary
    COG5048
    Location:173 → 417
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:314 → 334
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:368 → 390
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:382 → 407
    zf-H2C2_2; Zinc-finger double domain

  2. NM_170686.3 → NP_733787.1  zinc finger protein 398 isoform a

    See identical proteins and their annotated locations for NP_733787.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as p71-ZER6, represents the shorter transcript, and encodes the longer isoform a.
    Source sequence(s)
    AC004890, AK026380, AY049744
    Consensus CDS
    CCDS5894.1
    UniProtKB/Swiss-Prot
    A8K384, B4E377, Q8TD17, Q8TD18, Q9P2K7, Q9UDV8
    UniProtKB/TrEMBL
    A0A090N7S8
    Related
    ENSP00000420418.1, ENST00000475153.6
    Conserved Domains (4) summary
    smart00349
    Location:143 → 201
    KRAB; krueppel associated box
    COG5048
    Location:344 → 588
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:485 → 505
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cl25732
    Location:48 → 121
    SMC_N; RecF/RecN/SMC N terminal 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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    149126408..149183042
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011516440.3 → XP_011514742.1  zinc finger protein 398 isoform X2

    Conserved Domains (7) summary
    cd07765
    Location:136 → 175
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    smart00349
    Location:136 → 194
    KRAB; krueppel associated box
    COG5048
    Location:337 → 581
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:478 → 498
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:532 → 554
    zf-C2H2; Zinc finger, C2H2 type
    pfam12417
    Location:50 → 105
    DUF3669; Zinc finger protein
    pfam13465
    Location:546 → 571
    zf-H2C2_2; Zinc-finger double domain

  2. XM_011516439.3 → XP_011514741.1  zinc finger protein 398 isoform X1

    See identical proteins and their annotated locations for XP_011514741.1

    UniProtKB/TrEMBL
    B4DXA9
    Conserved Domains (7) summary
    cd07765
    Location:148 → 187
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    smart00349
    Location:148 → 206
    KRAB; krueppel associated box
    COG5048
    Location:349 → 593
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:490 → 510
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:544 → 566
    zf-C2H2; Zinc finger, C2H2 type
    pfam12417
    Location:62 → 117
    DUF3669; Zinc finger protein
    pfam13465
    Location:558 → 583
    zf-H2C2_2; Zinc-finger double domain

  3. XM_047420661.1 → XP_047276617.1  zinc finger protein 398 isoform X1

    UniProtKB/TrEMBL
    B4DXA9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    150308211..150364850
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054358719.1 → XP_054214694.1  zinc finger protein 398 isoform X2

  2. XM_054358718.1 → XP_054214693.1  zinc finger protein 398 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TD17.1 GenPept UniProtKB/Swiss-Prot:Q8TD17

Gene LinkOut

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