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

    Gene ID: 57541, updated on 3-May-2024

    Summary

    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
    NEW
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    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 
    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

    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)

    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_020781.4NP_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:173417
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:314334
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:368390
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:382407
      zf-H2C2_2; Zinc-finger double domain
    2. NM_170686.3NP_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:143201
      KRAB; krueppel associated box
      COG5048
      Location:344588
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:485505
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl25732
      Location:48121
      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_011516440.3XP_011514742.1  zinc finger protein 398 isoform X2

      Conserved Domains (7) summary
      cd07765
      Location:136175
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      smart00349
      Location:136194
      KRAB; krueppel associated box
      COG5048
      Location:337581
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:478498
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:532554
      zf-C2H2; Zinc finger, C2H2 type
      pfam12417
      Location:50105
      DUF3669; Zinc finger protein
      pfam13465
      Location:546571
      zf-H2C2_2; Zinc-finger double domain
    2. XM_011516439.3XP_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:148187
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      smart00349
      Location:148206
      KRAB; krueppel associated box
      COG5048
      Location:349593
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:490510
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:544566
      zf-C2H2; Zinc finger, C2H2 type
      pfam12417
      Location:62117
      DUF3669; Zinc finger protein
      pfam13465
      Location:558583
      zf-H2C2_2; Zinc-finger double domain
    3. XM_047420661.1XP_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_054358719.1XP_054214694.1  zinc finger protein 398 isoform X2

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