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    ZNF397 zinc finger protein 397 [ Homo sapiens (human) ]

    Gene ID: 84307, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ZNF397provided by HGNC
    Official Full Name
    zinc finger protein 397provided by HGNC
    Primary source
    HGNC:HGNC:18818
    See related
    Ensembl:ENSG00000186812 MIM:609601; AllianceGenome:HGNC:18818
    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
    ZNF47; ZSCAN15
    Summary
    This gene encodes a protein with a N-terminal SCAN domain, and the longer isoform contains nine C2H2-type zinc finger repeats in the C-terminal domain. The protein localizes to centromeres during interphase and early prophase, and different isoforms can repress or activate transcription in transfection studies. Multiple transcript variants encoding different isoforms have been found for this gene. Additional variants have been described, but their biological validity has not been determined. [provided by RefSeq, Oct 2009]
    Expression
    Ubiquitous expression in thyroid (RPKM 5.5), brain (RPKM 5.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZNF397 in Genome Data Viewer
    Location:
    18q12.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (35241034..35259227)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (35431795..35450511)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (32820998..32839191)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9394 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:32558231-32559430 Neighboring gene microtubule associated protein RP/EB family member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:32630340-32630840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:32718769-32719764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:32731753-32732253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13220 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:32785437-32786050 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:32786051-32786663 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:32820735-32821260 Neighboring gene zinc finger and SCAN domain containing 30 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13222 Neighboring gene zinc finger protein 271, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:32904859-32905554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13223 Neighboring gene uncharacterized LOC124904283 Neighboring gene zinc finger protein 24

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. ZNF397, a new class of interphase to early prophase-specific, SCAN-zinc-finger, mammalian centromere protein. Bailey SL, et al. Chromosoma, 2008 Aug. PMID 18369653
    2. Identification and characterization of two novel human SCAN domain-containing zinc finger genes ZNF396 and ZNF397. Wu Y, et al. Gene, 2003 May 22. PMID 12801647
    3. Clustering of C2-H2 zinc finger motif sequences within telomeric and fragile site regions of human chromosomes. Lichter P, et al. Genomics, 1992 Aug. PMID 1505991
    4. 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
    5. Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations. Connaughton DM, et al. Am J Hum Genet, 2020 Oct 1. PMID 32891193, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ZNF397, a new class of interphase to early prophase-specific, SCAN-zinc-finger, mammalian centromere protein.
      Title: ZNF397, a new class of interphase to early prophase-specific, SCAN-zinc-finger, mammalian centromere protein.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC13250

    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 cis-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 
    enables protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT involved_in regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    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
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in microtubule cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 397
    Names
    zinc finger and SCAN domain-containing protein 15
    zinc finger protein 47

    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_015815.1 RefSeqGene

      Range
      5005..13779
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001135178.3 → NP_001128650.1  zinc finger protein 397 isoform 1

      See identical proteins and their annotated locations for NP_001128650.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1), also known as ZNF397-fu.
      Source sequence(s)
      AC011815, AF533250, BC006172, BI772202
      Consensus CDS
      CCDS45852.1
      UniProtKB/Swiss-Prot
      Q8NF99, Q9BRM2
      Related
      ENSP00000331577.6, ENST00000330501.12
      Conserved Domains (6) summary
      smart00431
      Location:46 → 152
      SCAN; leucine rich region
      COG5048
      Location:278 → 527
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:399 → 419
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:285 → 307
      zf-C2H2; Zinc finger, C2H2 type
      pfam02023
      Location:46 → 134
      SCAN; SCAN domain
      pfam13465
      Location:299 → 323
      zf-H2C2_2; Zinc-finger double domain

    2. NM_032347.3 → NP_115723.1  zinc finger protein 397 isoform 2

      See identical proteins and their annotated locations for NP_115723.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an alternate 3' CDS and 3' UTR, as compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus that lacks the zinc finger domains, as compared to isoform 1.
      Source sequence(s)
      AA805259, AC011815, BC006172, BI772202
      Consensus CDS
      CCDS32814.1
      UniProtKB/TrEMBL
      Q96K65
      Related
      ENSP00000261333.5, ENST00000261333.10
      Conserved Domains (1) summary
      smart00431
      Location:46 → 152
      SCAN; leucine rich region

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      35241034..35259227
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011526229.3 → XP_011524531.1  zinc finger protein 397 isoform X1

      See identical proteins and their annotated locations for XP_011524531.1

      Conserved Domains (6) summary
      smart00431
      Location:46 → 139
      SCAN; leucine rich region
      COG5048
      Location:297 → 546
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:418 → 438
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:304 → 326
      zf-C2H2; Zinc finger, C2H2 type
      pfam02023
      Location:46 → 134
      SCAN; SCAN domain
      pfam13465
      Location:318 → 342
      zf-H2C2_2; Zinc-finger double domain

    2. XM_047437888.1 → XP_047293844.1  zinc finger protein 397 isoform X2

      UniProtKB/Swiss-Prot
      Q8NF99, Q9BRM2

    3. XM_006722558.3 → XP_006722621.1  zinc finger protein 397 isoform X1

      See identical proteins and their annotated locations for XP_006722621.1

      Conserved Domains (6) summary
      smart00431
      Location:46 → 139
      SCAN; leucine rich region
      COG5048
      Location:297 → 546
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:418 → 438
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:304 → 326
      zf-C2H2; Zinc finger, C2H2 type
      pfam02023
      Location:46 → 134
      SCAN; SCAN domain
      pfam13465
      Location:318 → 342
      zf-H2C2_2; Zinc-finger double domain

    4. XM_047437890.1 → XP_047293846.1  zinc finger protein 397 isoform X3

    5. XM_047437889.1 → XP_047293845.1  zinc finger protein 397 isoform X2

      UniProtKB/Swiss-Prot
      Q8NF99, Q9BRM2

    6. XM_011526230.3 → XP_011524532.1  zinc finger protein 397 isoform X1

      See identical proteins and their annotated locations for XP_011524532.1

      Conserved Domains (6) summary
      smart00431
      Location:46 → 139
      SCAN; leucine rich region
      COG5048
      Location:297 → 546
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:418 → 438
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:304 → 326
      zf-C2H2; Zinc finger, C2H2 type
      pfam02023
      Location:46 → 134
      SCAN; SCAN domain
      pfam13465
      Location:318 → 342
      zf-H2C2_2; Zinc-finger double domain

    7. XM_011526231.3 → XP_011524533.1  zinc finger protein 397 isoform X2

      See identical proteins and their annotated locations for XP_011524533.1

      UniProtKB/Swiss-Prot
      Q8NF99, Q9BRM2
      Conserved Domains (6) summary
      smart00431
      Location:46 → 152
      SCAN; leucine rich region
      COG5048
      Location:278 → 527
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:399 → 419
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:285 → 307
      zf-C2H2; Zinc finger, C2H2 type
      pfam02023
      Location:46 → 134
      SCAN; SCAN domain
      pfam13465
      Location:299 → 323
      zf-H2C2_2; Zinc-finger double domain

    8. XM_024451275.2 → XP_024307043.1  zinc finger protein 397 isoform X3

      Conserved Domains (2) summary
      COG5048
      Location:5 → 254
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:126 → 146
      ZF_C2H2; C2H2 Zn finger [structural motif]

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      35431795..35450511
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319274.1 → XP_054175249.1  zinc finger protein 397 isoform X2

      UniProtKB/Swiss-Prot
      Q8NF99, Q9BRM2

    2. XM_054319270.1 → XP_054175245.1  zinc finger protein 397 isoform X1

    3. XM_054319271.1 → XP_054175246.1  zinc finger protein 397 isoform X1

    4. XM_054319272.1 → XP_054175247.1  zinc finger protein 397 isoform X2

      UniProtKB/Swiss-Prot
      Q8NF99, Q9BRM2

    5. XM_054319269.1 → XP_054175244.1  zinc finger protein 397 isoform X1

    6. XM_054319275.1 → XP_054175250.1  zinc finger protein 397 isoform X3

    7. XM_054319273.1 → XP_054175248.1  zinc finger protein 397 isoform X2

      UniProtKB/Swiss-Prot
      Q8NF99, Q9BRM2

    8. XM_054319276.1 → XP_054175251.1  zinc finger protein 397 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NF99.2 GenPept UniProtKB/Swiss-Prot:Q8NF99

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

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