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    Zkscan3 zinc finger with KRAB and SCAN domains 3 [ Mus musculus (house mouse) ]

    Gene ID: 72739, updated on 22-Apr-2024

    Summary

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    Official Symbol
    Zkscan3provided by MGI
    Official Full Name
    zinc finger with KRAB and SCAN domains 3provided by MGI
    Primary source
    MGI:MGI:1919989
    See related
    Ensembl:ENSMUSG00000021327 AllianceGenome:MGI:1919989
    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
    Skz1; Zf47; Zfp-47; Zfp306; Zfp307; mszf35; 2810435N07Rik
    Summary
    Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and identical protein binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within autophagy. Predicted to be located in cytoplasm and nucleoplasm. Is expressed in several structures, including central nervous system; early conceptus; genitourinary system; and retina nuclear layer. Orthologous to several human genes including ZKSCAN3 (zinc finger with KRAB and SCAN domains 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 18.0), limb E14.5 (RPKM 16.1) and 28 other tissues See more
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    Genomic context

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    Location:
    13 A3.1; 13 7.78 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 13 NC_000079.7 (21571174..21586942, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (21387004..21402755, complement)

    Chromosome 13 - NC_000079.7Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 2 subfamily B member 28 Neighboring gene zinc finger and SCAN domain containing 12 Neighboring gene STARR-seq mESC enhancer starr_33849 Neighboring gene STARR-positive B cell enhancer ABC_E10783 Neighboring gene microRNA 6942 Neighboring gene piggyBac transposable element derived 1 Neighboring gene RIKEN cDNA 4930470G03 gene Neighboring gene zinc finger and SCAN domain containing 26 Neighboring gene microRNA 1896

    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. Cardiomyocyte ZKSCAN3 regulates remodeling following pressure-overload. Ouyang X, et al. Physiol Rep, 2023 May. PMID 37144628, Free PMC Article
    2. The kidney-expressed transcription factor ZKSCAN3 is dispensable for autophagy transcriptional regulation and AKI progression in mouse. Liu Z, et al. Mutat Res, 2022 Jul-Dec. PMID 35841832
    3. The role of ZKSCAN3 in the transcriptional regulation of autophagy. Pan H, et al. Autophagy, 2017 Jul 3. PMID 28581889, Free PMC Article
    4. Effect of Lacking ZKSCAN3 on Autophagy, Lysosomal Biogenesis and Senescence. Li XM, et al. Int J Mol Sci, 2023 Apr 24. PMID 37175493, Free PMC Article
    5. Deacetylation of ZKSCAN3 by SIRT1 induces autophagy and protects SN4741 cells against MPP(+)-induced oxidative stress. Wu X, et al. Free Radic Biol Med, 2022 Mar. PMID 35124181

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ALKBH5 suppresses autophagic flux via N6-methyladenosine demethylation of ZKSCAN3 mRNA in acute pancreatitis.
      Title: ALKBH5 suppresses autophagic flux via N6-methyladenosine demethylation of ZKSCAN3 mRNA in acute pancreatitis.
    2. Effect of Lacking ZKSCAN3 on Autophagy, Lysosomal Biogenesis and Senescence.
      Title: Effect of Lacking ZKSCAN3 on Autophagy, Lysosomal Biogenesis and Senescence.
    3. Cardiomyocyte ZKSCAN3 regulates remodeling following pressure-overload.
      Title: Cardiomyocyte ZKSCAN3 regulates remodeling following pressure-overload.
    4. The kidney-expressed transcription factor ZKSCAN3 is dispensable for autophagy transcriptional regulation and AKI progression in mouse.
      Title: The kidney-expressed transcription factor ZKSCAN3 is dispensable for autophagy transcriptional regulation and AKI progression in mouse.
    5. Zkscan3 affects erythroblast development by regulating the transcriptional activity of GATA1 and KLF1 in mice.
      Title: Zkscan3 affects erythroblast development by regulating the transcriptional activity of GATA1 and KLF1 in mice.
    6. Deacetylation of ZKSCAN3 by SIRT1 induces autophagy and protects SN4741 cells against MPP(+)-induced oxidative stress.
      Title: Deacetylation of ZKSCAN3 by SIRT1 induces autophagy and protects SN4741 cells against MPP(+)-induced oxidative stress.
    7. ZKSCAN3 in severe bacterial lung infection and sepsis-induced immunosuppression.
      Title: ZKSCAN3 in severe bacterial lung infection and sepsis-induced immunosuppression.
    8. a mouse model lacking Zkscan3 expression, is reported.
      Title: The role of ZKSCAN3 in the transcriptional regulation of autophagy.
    9. ZKSCAN3 regulates the expression of several genes favoring tumor progression including integrin beta 4 and VEGF
      Title: Unbiased screening for transcriptional targets of ZKSCAN3 identifies integrin beta 4 and vascular endothelial growth factor as downstream targets.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein with KRAB and SCAN domains 3
    Names
    SCAN-KRAB-zinc finger gene 1
    SCAN-KRAB-zinc finger protein
    zinc finger protein 306
    zinc finger protein 307
    zinc finger protein 47 homolog

    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_001145778.2 → NP_001139250.1  zinc finger protein with KRAB and SCAN domains 3 isoform a

      See identical proteins and their annotated locations for NP_001139250.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AI132359, AK028902, AK031286, BX001068
      Consensus CDS
      CCDS26274.1
      UniProtKB/Swiss-Prot
      Q3V3Z2, Q8CD81, Q91VW9, Q9ESY5
      UniProtKB/TrEMBL
      A0A0R4J1L3
      Related
      ENSMUSP00000068424.9, ENSMUST00000070785.16
      Conserved Domains (6) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region
      COG5048
      Location:367 → 514
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:371 → 391
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:507 → 529
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:328 → 350
      zf-H2C2_2; Zinc-finger double domain
      cl02581
      Location:213 → 267
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    2. NM_001368182.1 → NP_001355111.1  zinc finger protein with KRAB and SCAN domains 3 isoform b

      Status: VALIDATED

      Source sequence(s)
      AI132359, AK028902, BX001068, CK627138
      Consensus CDS
      CCDS88419.1
      UniProtKB/TrEMBL
      A0A286YD32
      Related
      ENSMUSP00000153241.2, ENSMUST00000223831.2

    3. NM_023685.5 → NP_076174.3  zinc finger protein with KRAB and SCAN domains 3 isoform a

      See identical proteins and their annotated locations for NP_076174.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses a different splice site in the 5' UTR, compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AI132359, AK028902, BX001068
      Consensus CDS
      CCDS26274.1
      UniProtKB/Swiss-Prot
      Q3V3Z2, Q8CD81, Q91VW9, Q9ESY5
      UniProtKB/TrEMBL
      A0A0R4J1L3
      Related
      ENSMUSP00000112135.4, ENSMUST00000116434.11
      Conserved Domains (6) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region
      COG5048
      Location:367 → 514
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:371 → 391
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:507 → 529
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:328 → 350
      zf-H2C2_2; Zinc-finger double domain
      cl02581
      Location:213 → 267
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    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_000079.7 Reference GRCm39 C57BL/6J

      Range
      21571174..21586942 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006516790.5 → XP_006516853.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      See identical proteins and their annotated locations for XP_006516853.1

      UniProtKB/Swiss-Prot
      Q3V3Z2, Q8CD81, Q91VW9, Q9ESY5
      UniProtKB/TrEMBL
      A0A0R4J1L3
      Conserved Domains (6) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region
      COG5048
      Location:367 → 514
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:371 → 391
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:507 → 529
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:328 → 350
      zf-H2C2_2; Zinc-finger double domain
      cl02581
      Location:213 → 267
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    2. XM_006516789.5 → XP_006516852.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      See identical proteins and their annotated locations for XP_006516852.1

      UniProtKB/Swiss-Prot
      Q3V3Z2, Q8CD81, Q91VW9, Q9ESY5
      UniProtKB/TrEMBL
      A0A0R4J1L3
      Conserved Domains (6) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region
      COG5048
      Location:367 → 514
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:371 → 391
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:507 → 529
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:328 → 350
      zf-H2C2_2; Zinc-finger double domain
      cl02581
      Location:213 → 267
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    3. XM_006516792.4 → XP_006516855.1  zinc finger protein with KRAB and SCAN domains 3 isoform X2

      UniProtKB/TrEMBL
      Q9CSC5
      Conserved Domains (4) summary
      COG5048
      Location:113 → 260
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:117 → 137
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:253 → 275
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:74 → 96
      zf-H2C2_2; Zinc-finger double domain

    4. XM_036158185.1 → XP_036014078.1  zinc finger protein with KRAB and SCAN domains 3 isoform X3

      UniProtKB/TrEMBL
      D3YTV4, Q5RJ53
      Conserved Domains (2) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region
      cl02581
      Location:213 → 251
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    5. XM_036158186.1 → XP_036014079.1  zinc finger protein with KRAB and SCAN domains 3 isoform X3

      UniProtKB/TrEMBL
      D3YTV4, Q5RJ53
      Related
      ENSMUSP00000112134.2, ENSMUST00000116433.2
      Conserved Domains (2) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region
      cl02581
      Location:213 → 251
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    6. XM_036158187.1 → XP_036014080.1  zinc finger protein with KRAB and SCAN domains 3 isoform X3

      UniProtKB/TrEMBL
      D3YTV4, Q5RJ53
      Related
      ENSMUSP00000112862.2, ENSMUST00000117721.8
      Conserved Domains (2) summary
      smart00431
      Location:47 → 159
      SCAN; leucine rich region
      cl02581
      Location:213 → 251
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q91VW9.1 GenPept UniProtKB/Swiss-Prot:Q91VW9

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