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

    Gene ID: 80317, updated on 10-Dec-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 DNA-templated transcription. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    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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    See ZKSCAN3 in Genome Data Viewer
    Location:
    6p22.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (28349878..28369172)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (28221444..28240735)
    RS_2024_09 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: 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. 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. Expression of ZKSCAN3 protein suppresses proliferation, migration, and invasion of pancreatic cancer through autophagy. Nonoyama K, et al. Cancer Sci, 2024 Jun. PMID 38671550, Free PMC Article
    3. The previously undescribed ZKSCAN3 (ZNF306) is a novel "driver" of colorectal cancer progression. Yang L, et al. Cancer Res, 2008 Jun 1. PMID 18519692
    4. Evidence of a role for the novel zinc-finger transcription factor ZKSCAN3 in modulating Cyclin D2 expression in multiple myeloma. Yang L, et al. Oncogene, 2011 Mar 17. PMID 21057542, Free PMC Article
    5. The zinc finger transcription factor ZKSCAN3 promotes prostate cancer cell migration. Zhang X, et al. Int J Biochem Cell Biol, 2012 Jul. PMID 22531714, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expression of ZKSCAN3 protein suppresses proliferation, migration, and invasion of pancreatic cancer through autophagy.
      Title: Expression of ZKSCAN3 protein suppresses proliferation, migration, and invasion of pancreatic cancer through autophagy.
    2. Effect of Lacking ZKSCAN3 on Autophagy, Lysosomal Biogenesis and Senescence.
      Title: Effect of Lacking ZKSCAN3 on Autophagy, Lysosomal Biogenesis and Senescence.
    3. 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.
    4. CHD1L augments autophagy-mediated migration of hepatocellular carcinoma through targeting ZKSCAN3.
      Title: CHD1L augments autophagy-mediated migration of hepatocellular carcinoma through targeting ZKSCAN3.
    5. 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.
    6. 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.
    7. ZKSCAN3 counteracts cellular senescence by stabilizing heterochromatin.
      Title: ZKSCAN3 counteracts cellular senescence by stabilizing heterochromatin.
    8. 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.
    9. ZKSCAN3 plays a significant role in the progression of breast cancer
      Title: ZKSCAN3 promotes breast cancer cell proliferation, migration and invasion.
    10. These results suggest that ZKSCAN3 plays an important role in bladder cancer outgrowth
      Title: ZKSCAN3 promotes bladder cancer cell proliferation, migration, and invasion.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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)

    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_2024_08

    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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