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    Zfp398 zinc finger protein 398 [ Mus musculus (house mouse) ]

    Gene ID: 272347, updated on 30-Apr-2024

    Summary

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    Official Symbol
    Zfp398provided by MGI
    Official Full Name
    zinc finger protein 398provided by MGI
    Primary source
    MGI:MGI:1917856
    See related
    Ensembl:ENSMUSG00000062519 AllianceGenome:MGI:1917856
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    5730513I23Rik
    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. Is expressed in several structures, including branchial arch; central nervous system; early conceptus; genitourinary system; and sensory organ. Orthologous to human ZNF398 (zinc finger protein 398). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in ovary adult (RPKM 4.0), thymus adult (RPKM 3.6) and 28 other tissues See more
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    Genomic context

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    See Zfp398 in Genome Data Viewer
    Location:
    6 B2.3; 6 22.94 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (47812567..47850476)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (47835633..47873542)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene protein disulfide isomerase associated 4 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:47763598-47763839 Neighboring gene microRNA 704 Neighboring gene ribosomal protein L35A, pseudogene 7 Neighboring gene STARR-seq mESC enhancer starr_15785 Neighboring gene zinc finger protein 786 Neighboring gene zinc finger protein 282 Neighboring gene predicted gene, 52899 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: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. Guo G, et al. Dev Cell, 2010 Apr 20. PMID 20412781
    2. An atlas of combinatorial transcriptional regulation in mouse and man. Ravasi T, et al. Cell, 2010 Mar 5. PMID 20211142, Free PMC Article
    3. A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. Yokoyama S, et al. Dev Cell, 2009 Dec. PMID 20059953, Free PMC Article
    4. Mouse brain organization revealed through direct genome-scale TF expression analysis. Gray PA, et al. Science, 2004 Dec 24. PMID 15618518
    5. GUDMAP: the genitourinary developmental molecular anatomy project. McMahon AP, et al. J Am Soc Nephrol, 2008 Apr. PMID 18287559

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (3) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • 6430539K21

    Gene Ontology Provided by MGI

    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
    		  
    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
    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 398

    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_027477.3 → NP_081753.1  zinc finger protein 398 isoform 1

      See identical proteins and their annotated locations for NP_081753.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK046208, AK078250, AK081169, BB066614
      Consensus CDS
      CCDS20099.1
      UniProtKB/TrEMBL
      Q14DQ6, Q8BV16
      Related
      ENSMUSP00000078806.5, ENSMUST00000079881.11
      Conserved Domains (6) summary
      cd07765
      Location:143 → 182
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      smart00349
      Location:143 → 203
      KRAB; krueppel associated box
      COG5048
      Location:368 → 588
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:486 → 506
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:540 → 562
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:554 → 579
      zf-H2C2_2; Zinc-finger double domain

    2. NM_173034.3 → NP_766622.2  zinc finger protein 398 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which lacks an internal segment and is shorter, compared to isoform 1.
      Source sequence(s)
      AK046208, AK078250, BB066614, BB640605
      Consensus CDS
      CCDS39476.1
      UniProtKB/TrEMBL
      E9Q569, Q8BVH0
      Related
      ENSMUSP00000110245.2, ENSMUST00000114598.3
      Conserved Domains (4) summary
      smart00349
      Location:11 → 71
      KRAB; krueppel associated box
      COG5048
      Location:236 → 456
      COG5048; FOG: Zn-finger [General function prediction only]
      PRK05580
      Location:211 → 244
      PRK05580; primosome assembly protein PriA; Validated
      sd00017
      Location:354 → 374
      ZF_C2H2; C2H2 Zn finger [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000072.7 Reference GRCm39 C57BL/6J

      Range
      47812567..47850476
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030255435.1 → XP_030111295.1  zinc finger protein 398 isoform X1

      UniProtKB/TrEMBL
      Q8BVH0
      Conserved Domains (4) summary
      smart00349
      Location:14 → 74
      KRAB; krueppel associated box
      COG5048
      Location:239 → 459
      COG5048; FOG: Zn-finger [General function prediction only]
      PRK05580
      Location:214 → 247
      PRK05580; primosome assembly protein PriA; Validated
      sd00017
      Location:357 → 377
      ZF_C2H2; C2H2 Zn finger [structural motif]

    2. XM_006506208.4 → XP_006506271.1  zinc finger protein 398 isoform X2

      UniProtKB/TrEMBL
      Q8BVH0
      Conserved Domains (3) summary
      COG5048
      Location:197 → 417
      COG5048; FOG: Zn-finger [General function prediction only]
      PRK05580
      Location:172 → 205
      PRK05580; primosome assembly protein PriA; Validated
      sd00017
      Location:315 → 335
      ZF_C2H2; C2H2 Zn finger [structural motif]
    Nucleotide Protein Strain
    Heading Accession and Version

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