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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.
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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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