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

Gene ID: 84307, updated on 5-Mar-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
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Genomic context

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Location:
18q12.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (35241034..35259227)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (35431795..35450511)
105.20220307 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: 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. 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. 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
  5. Mutual regulation between OGT and XIAP to control colon cancer cell growth and invasion. Seo HG, et al. Cell Death Dis, 2020 Sep 29. PMID 32994395, Free PMC Article

See all (22) 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)

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

  • 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 
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
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 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_2023_10

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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