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

    Gene ID: 57541, updated on 2-Nov-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (149126408..149183042)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (150308211..150364850)
    RS_2024_09 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 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. The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification. Helleboid PY, et al. EMBO J, 2019 Sep 16. PMID 31403225, Free PMC Article

    See all (24) 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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    NEW Try the new Transcript table

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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