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ZKSCAN3 zinc finger with KRAB and SCAN domains 3 [ Homo sapiens (human) ]

Gene ID: 80317, updated on 5-Mar-2024

Summary

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Official Symbol
ZKSCAN3provided by HGNC
Official Full Name
zinc finger with KRAB and SCAN domains 3provided by HGNC
Primary source
HGNC:HGNC:13853
See related
Ensembl:ENSG00000189298 MIM:612791; AllianceGenome:HGNC:13853
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ZF47; Zfp47; ZFP306; ZNF306; ZNF309; zfp-47; ZSCAN13; ZSCAN35; dJ874C20.1; dJ874C20.1.
Summary
Enables DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in several processes, including negative regulation of autophagy; negative regulation of cellular senescence; and regulation of transcription, DNA-templated. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 1.5), ovary (RPKM 1.5) and 25 other tissues See more
Orthologs
all
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Genomic context

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Location:
6p22.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (28349878..28369172)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (28221444..28240735)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (28317724..28336949)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17044 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:28249721-28249897 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:28251848-28252055 Neighboring gene piggyBac transposable element derived 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:28278749-28279250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:28279251-28279750 Neighboring gene SMIM15 pseudogene 2 Neighboring gene zinc finger and SCAN domain containing 31 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:28321865-28322364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24355 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:28324191-28325095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24356 Neighboring gene zinc finger and SCAN domain containing 12 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17045 Neighboring gene uncharacterized LOC105374998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24357

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. Context-dependent pro- and anti-resection roles of ZKSCAN3 in the regulation of fork processing during replication stress. Yang Z, et al. J Biol Chem, 2022 Aug. PMID 35779634, Free PMC Article
  2. ZKSCAN3 counteracts cellular senescence by stabilizing heterochromatin. Hu H, et al. Nucleic Acids Res, 2020 Jun 19. PMID 32427330, Free PMC Article
  3. Prognostic Significance of ZKSCAN3 (ZNF306) Expression in Gastric Carcinoma. Takano Y, et al. Anticancer Res, 2020 Jan. PMID 31892555
  4. ZKSCAN3 promotes breast cancer cell proliferation, migration and invasion. Chi Y, et al. Biochem Biophys Res Commun, 2018 Sep 18. PMID 30049438
  5. ZKSCAN3 promotes bladder cancer cell proliferation, migration, and invasion. Kawahara T, et al. Oncotarget, 2016 Aug 16. PMID 27447553, Free PMC Article

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Effect of Lacking ZKSCAN3 on Autophagy, Lysosomal Biogenesis and Senescence.
    Title: Effect of Lacking ZKSCAN3 on Autophagy, Lysosomal Biogenesis and Senescence.
  2. Context-dependent pro- and anti-resection roles of ZKSCAN3 in the regulation of fork processing during replication stress.
    Title: Context-dependent pro- and anti-resection roles of ZKSCAN3 in the regulation of fork processing during replication stress.
  3. CHD1L augments autophagy-mediated migration of hepatocellular carcinoma through targeting ZKSCAN3.
    Title: CHD1L augments autophagy-mediated migration of hepatocellular carcinoma through targeting ZKSCAN3.
  4. Role of the Transcriptional Repressor Zinc Finger with KRAB and SCAN Domains 3 (ZKSCAN3) in Retinal Pigment Epithelial Cells.
    Title: Role of the Transcriptional Repressor Zinc Finger with KRAB and SCAN Domains 3 (ZKSCAN3) in Retinal Pigment Epithelial Cells.
  5. Human ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors in autophagy regulation.
    Title: Human ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors in autophagy regulation.
  6. ZKSCAN3 counteracts cellular senescence by stabilizing heterochromatin.
    Title: ZKSCAN3 counteracts cellular senescence by stabilizing heterochromatin.
  7. overexpression of ZKSCAN3 was frequently observed in gastric cancer cells and was significantly correlatedwith poorer clinical prognosis of patients with gastric cancer.
    Title: Prognostic Significance of ZKSCAN3 (ZNF306) Expression in Gastric Carcinoma.
  8. ZKSCAN3 plays a significant role in the progression of breast cancer
    Title: ZKSCAN3 promotes breast cancer cell proliferation, migration and invasion.
  9. These results suggest that ZKSCAN3 plays an important role in bladder cancer outgrowth
    Title: ZKSCAN3 promotes bladder cancer cell proliferation, migration, and invasion.
  10. ZKSCAN3 appears to promote colorectal tumor progression and invasion. ZKSCAN3 may facilitate hepatic metastasis of CRC associated with CEA particularly in cases with CEA-producing tumor
    Title: ZKSCAN3 Facilitates Liver Metastasis of Colorectal Cancer Associated with CEA-expressing Tumor.
Submit: New GeneRIF Correction See all GeneRIFs (14)

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

EBI GWAS Catalog

Description
Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
EBI GWAS Catalog

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

  • FLJ33906, KIAA0426

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in autophagy IEA
Inferred from Electronic Annotation
more info
  
involved_in lysosome organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of autophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of cellular senescence IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive 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 nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
zinc finger protein with KRAB and SCAN domains 3
Names
zinc finger and SCAN domain-containing protein 13
zinc finger protein 306
zinc finger protein 309
zinc finger protein 47 homolog
zinc finger protein zfp47

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_001242894.2 → NP_001229823.1  zinc finger protein with KRAB and SCAN domains 3 isoform 1

    See identical proteins and their annotated locations for NP_001229823.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AK313532, AL021997, AL358785, DA440043
    Consensus CDS
    CCDS4650.1
    UniProtKB/Swiss-Prot
    B2R8W2, B3KVC0, H7BXX1, Q5VXH3, Q92972, Q9BRR0, Q9H4T3
    Related
    ENSP00000366465.1, ENST00000377255.3
    Conserved Domains (8) summary
    smart00431
    Location:42 → 154
    SCAN; leucine rich region
    smart00349
    Location:214 → 274
    KRAB; krueppel associated box
    COG5048
    Location:368 → 515
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:372 → 392
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:314 → 336
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:217 → 252
    KRAB; KRAB box
    pfam02023
    Location:42 → 130
    SCAN; SCAN domain
    pfam13465
    Location:384 → 409
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001242895.2 → NP_001229824.1  zinc finger protein with KRAB and SCAN domains 3 isoform 2

    See identical proteins and their annotated locations for NP_001229824.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon compared to variant 1. The resulting protein (isoform 2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK122790, AL021997, AL358785, DA440043
    Consensus CDS
    CCDS56408.1
    UniProtKB/Swiss-Prot
    Q9BRR0
    Related
    ENSP00000341883.5, ENST00000341464.9
    Conserved Domains (6) summary
    smart00349
    Location:66 → 126
    KRAB; krueppel associated box
    COG5048
    Location:220 → 367
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:224 → 244
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:166 → 188
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:69 → 104
    KRAB; KRAB box
    pfam13465
    Location:236 → 261
    zf-H2C2_2; Zinc-finger double domain

  3. NM_024493.4 → NP_077819.2  zinc finger protein with KRAB and SCAN domains 3 isoform 1

    See identical proteins and their annotated locations for NP_077819.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein (isoform 1).
    Source sequence(s)
    AL021997, AL358785, BC006118, DA440043
    Consensus CDS
    CCDS4650.1
    UniProtKB/Swiss-Prot
    B2R8W2, B3KVC0, H7BXX1, Q5VXH3, Q92972, Q9BRR0, Q9H4T3
    Related
    ENSP00000252211.2, ENST00000252211.7
    Conserved Domains (8) summary
    smart00431
    Location:42 → 154
    SCAN; leucine rich region
    smart00349
    Location:214 → 274
    KRAB; krueppel associated box
    COG5048
    Location:368 → 515
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:372 → 392
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:314 → 336
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:217 → 252
    KRAB; KRAB box
    pfam02023
    Location:42 → 130
    SCAN; SCAN domain
    pfam13465
    Location:384 → 409
    zf-H2C2_2; Zinc-finger double 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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    28349878..28369172
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715215.3 → XP_006715278.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

    See identical proteins and their annotated locations for XP_006715278.1

    UniProtKB/Swiss-Prot
    B2R8W2, B3KVC0, H7BXX1, Q5VXH3, Q92972, Q9BRR0, Q9H4T3
    Conserved Domains (8) summary
    smart00431
    Location:42 → 154
    SCAN; leucine rich region
    smart00349
    Location:214 → 274
    KRAB; krueppel associated box
    COG5048
    Location:368 → 515
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:372 → 392
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:314 → 336
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:217 → 252
    KRAB; KRAB box
    pfam02023
    Location:42 → 130
    SCAN; SCAN domain
    pfam13465
    Location:384 → 409
    zf-H2C2_2; Zinc-finger double domain

  2. XM_047419375.1 → XP_047275331.1  zinc finger protein with KRAB and SCAN domains 3 isoform X2

  3. XM_047419376.1 → XP_047275332.1  zinc finger protein with KRAB and SCAN domains 3 isoform X4

  4. XM_047419373.1 → XP_047275329.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

    UniProtKB/Swiss-Prot
    B2R8W2, B3KVC0, H7BXX1, Q5VXH3, Q92972, Q9BRR0, Q9H4T3

  5. XM_047419374.1 → XP_047275330.1  zinc finger protein with KRAB and SCAN domains 3 isoform X2

  6. XM_005249423.4 → XP_005249480.1  zinc finger protein with KRAB and SCAN domains 3 isoform X3

    Conserved Domains (6) summary
    smart00349
    Location:81 → 141
    KRAB; krueppel associated box
    COG5048
    Location:235 → 382
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:239 → 259
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:181 → 203
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:84 → 119
    KRAB; KRAB box
    pfam13465
    Location:251 → 276
    zf-H2C2_2; Zinc-finger double domain

  7. XM_006715218.4 → XP_006715281.1  zinc finger protein with KRAB and SCAN domains 3 isoform X4

    See identical proteins and their annotated locations for XP_006715281.1

    UniProtKB/Swiss-Prot
    Q9BRR0
    Conserved Domains (6) summary
    smart00349
    Location:66 → 126
    KRAB; krueppel associated box
    COG5048
    Location:220 → 367
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:224 → 244
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:166 → 188
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:69 → 104
    KRAB; KRAB box
    pfam13465
    Location:236 → 261
    zf-H2C2_2; Zinc-finger double domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    28221444..28240735
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356459.1 → XP_054212434.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

  2. XM_054356462.1 → XP_054212437.1  zinc finger protein with KRAB and SCAN domains 3 isoform X2

  3. XM_054356460.1 → XP_054212435.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

  4. XM_054356461.1 → XP_054212436.1  zinc finger protein with KRAB and SCAN domains 3 isoform X2

  5. XM_054356464.1 → XP_054212439.1  zinc finger protein with KRAB and SCAN domains 3 isoform X4

  6. XM_054356463.1 → XP_054212438.1  zinc finger protein with KRAB and SCAN domains 3 isoform X3

  7. XM_054356465.1 → XP_054212440.1  zinc finger protein with KRAB and SCAN domains 3 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BRR0.2 GenPept UniProtKB/Swiss-Prot:Q9BRR0

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