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    ZKSCAN4 zinc finger with KRAB and SCAN domains 4 [ Homo sapiens (human) ]

    Gene ID: 387032, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ZKSCAN4provided by HGNC
    Official Full Name
    zinc finger with KRAB and SCAN domains 4provided by HGNC
    Primary source
    HGNC:HGNC:13854
    See related
    Ensembl:ENSG00000187626 MIM:611643; AllianceGenome:HGNC:13854
    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
    ZNF307; ZNF427; ZSCAN36; P1P373C6
    Summary
    Enables identical protein binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 2.9), spleen (RPKM 2.1) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZKSCAN4 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 (28241697..28259211, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (28113435..28131010, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (28209475..28226989, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr6:28184762-28184955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24348 Neighboring gene transducer of ERBB2, 2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24349 Neighboring gene zinc finger and SCAN domain containing 9 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:28203630-28204444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17042 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17043 Neighboring gene NFKB activating protein like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24352 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:28234963-28235527 Neighboring gene zinc finger and SCAN domain containing 26

    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 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. ZNF307 (Zinc Finger Protein 307) Acts as a Negative Regulator of Pressure Overload-Induced Cardiac Hypertrophy. Yu CJ, et al. Hypertension, 2017 Apr. PMID 28223477
    2. Zinc finger protein 307 functions as a tumor‑suppressor and inhibits cell proliferation by inducing apoptosis in hepatocellular carcinoma. Liang Y, et al. Oncol Rep, 2017 Oct. PMID 28765950
    3. ZNF307, a novel zinc finger gene suppresses p53 and p21 pathway. Li J, et al. Biochem Biophys Res Commun, 2007 Nov 30. PMID 17910948
    4. A RAS recruitment screen identifies ZKSCAN4 as a glucocorticoid receptor-interacting protein. Ecker K, et al. J Mol Endocrinol, 2009 Feb. PMID 19008334
    5. Genome-wide association study identifies a susceptibility locus for schizophrenia in Han Chinese at 11p11.2. Yue WH, et al. Nat Genet, 2011 Oct 30. PMID 22037552

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. our results indicate that ZNF307 may serve as a tumor suppressor and inhibits cell proliferation of hepatocellular carcinoma via inducing apoptosis
      Title: Zinc finger protein 307 functions as a tumor‑suppressor and inhibits cell proliferation by inducing apoptosis in hepatocellular carcinoma.
    2. ZNF307 ameliorates pressure overload-induced cardiac hypertrophy by inhibiting the activity of NF-kappaB-signaling pathway
      Title: ZNF307 (Zinc Finger Protein 307) Acts as a Negative Regulator of Pressure Overload-Induced Cardiac Hypertrophy.
    3. The SCAN- and KRAB-domain-containing zinc finger protein 307 (ZKSCAN4) was co-precipitated with the receptor when both proteins were overexpressed in HEK293 cells.
      Title: A RAS recruitment screen identifies ZKSCAN4 as a glucocorticoid receptor-interacting protein.
    4. ZNF307 might suppress p53-p21 pathway through activating MDM2 and EP300 expression and inducing p53 degradation
      Title: ZNF307, a novel zinc finger gene suppresses p53 and p21 pathway.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies a susceptibility locus for schizophrenia in Han Chinese at 11p11.2.
    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

    • FLJ32136

    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 identical protein binding IPI
    Inferred from Physical Interaction
    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 
    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 nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein with KRAB and SCAN domains 4
    Names
    p373c6.1 (novel C2H2 type zinc finger protein)
    zinc finger protein 307
    zinc finger protein 427

    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_001304506.2 → NP_001291435.1  zinc finger protein with KRAB and SCAN domains 4 isoform 2

      See identical proteins and their annotated locations for NP_001291435.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate 5'-terminal exon and a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AK302017, AL022393
      UniProtKB/TrEMBL
      B7Z7H3, C9JSR9
      Conserved Domains (6) summary
      smart00349
      Location:66 → 126
      KRAB; krueppel associated box
      COG5048
      Location:219 → 389
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:223 → 243
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:165 → 187
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:69 → 104
      KRAB; KRAB box
      pfam13465
      Location:235 → 260
      zf-H2C2_2; Zinc-finger double domain

    2. NM_019110.5 → NP_061983.2  zinc finger protein with KRAB and SCAN domains 4 isoform 1

      See identical proteins and their annotated locations for NP_061983.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL022393, AY781778, HY070446
      Consensus CDS
      CCDS4647.1
      UniProtKB/Swiss-Prot
      B2RE32, Q5U7L4, Q969J2
      UniProtKB/TrEMBL
      A0A0S2Z658
      Related
      ENSP00000366509.2, ENST00000377294.3
      Conserved Domains (6) summary
      smart00431
      Location:49 → 160
      SCAN; leucine rich region
      smart00349
      Location:221 → 281
      KRAB; krueppel associated box
      COG5048
      Location:374 → 544
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:378 → 398
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:320 → 342
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:335 → 357
      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
      28241697..28259211 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418753.1 → XP_047274709.1  zinc finger protein with KRAB and SCAN domains 4 isoform X5

      UniProtKB/TrEMBL
      B7Z7H3, C9JSR9

    2. XM_047418754.1 → XP_047274710.1  zinc finger protein with KRAB and SCAN domains 4 isoform X4

    3. XM_005249095.4 → XP_005249152.1  zinc finger protein with KRAB and SCAN domains 4 isoform X1

      See identical proteins and their annotated locations for XP_005249152.1

      UniProtKB/Swiss-Prot
      B2RE32, Q5U7L4, Q969J2
      UniProtKB/TrEMBL
      A0A0S2Z658
      Conserved Domains (6) summary
      smart00431
      Location:49 → 160
      SCAN; leucine rich region
      smart00349
      Location:221 → 281
      KRAB; krueppel associated box
      COG5048
      Location:374 → 544
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:378 → 398
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:320 → 342
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:335 → 357
      zf-H2C2_2; Zinc-finger double domain

    4. XM_005249098.4 → XP_005249155.1  zinc finger protein with KRAB and SCAN domains 4 isoform X3

      See identical proteins and their annotated locations for XP_005249155.1

      Conserved Domains (5) summary
      smart00349
      Location:118 → 178
      KRAB; krueppel associated box
      COG5048
      Location:271 → 441
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:275 → 295
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:217 → 239
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:232 → 254
      zf-H2C2_2; Zinc-finger double domain

    5. XM_011514588.4 → XP_011512890.1  zinc finger protein with KRAB and SCAN domains 4 isoform X2

      Conserved Domains (8) summary
      smart00431
      Location:49 → 131
      SCAN; leucine rich region
      smart00349
      Location:192 → 252
      KRAB; krueppel associated box
      COG5048
      Location:345 → 515
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:349 → 369
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:347 → 369
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:195 → 230
      KRAB; KRAB box
      pfam02023
      Location:49 → 113
      SCAN; SCAN domain
      pfam13465
      Location:361 → 386
      zf-H2C2_2; Zinc-finger double domain

    6. XM_011514589.3 → XP_011512891.1  zinc finger protein with KRAB and SCAN domains 4 isoform X5

      See identical proteins and their annotated locations for XP_011512891.1

      UniProtKB/TrEMBL
      B7Z7H3, C9JSR9
      Conserved Domains (6) summary
      smart00349
      Location:66 → 126
      KRAB; krueppel associated box
      COG5048
      Location:219 → 389
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:223 → 243
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:165 → 187
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:69 → 104
      KRAB; KRAB box
      pfam13465
      Location:235 → 260
      zf-H2C2_2; Zinc-finger double domain

    7. XM_047418755.1 → XP_047274711.1  zinc finger protein with KRAB and SCAN domains 4 isoform X5

      UniProtKB/TrEMBL
      B7Z7H3, C9JSR9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      28113435..28131010 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355386.1 → XP_054211361.1  zinc finger protein with KRAB and SCAN domains 4 isoform X6

    2. XM_054355390.1 → XP_054211365.1  zinc finger protein with KRAB and SCAN domains 4 isoform X4

    3. XM_054355387.1 → XP_054211362.1  zinc finger protein with KRAB and SCAN domains 4 isoform X1

      UniProtKB/Swiss-Prot
      B2RE32, Q5U7L4, Q969J2
      UniProtKB/TrEMBL
      A0A0S2Z658

    4. XM_054355389.1 → XP_054211364.1  zinc finger protein with KRAB and SCAN domains 4 isoform X3

    5. XM_054355388.1 → XP_054211363.1  zinc finger protein with KRAB and SCAN domains 4 isoform X2

    6. XM_054355392.1 → XP_054211367.1  zinc finger protein with KRAB and SCAN domains 4 isoform X5

      UniProtKB/TrEMBL
      B7Z7H3, C9JSR9

    7. XM_054355391.1 → XP_054211366.1  zinc finger protein with KRAB and SCAN domains 4 isoform X5

      UniProtKB/TrEMBL
      B7Z7H3, C9JSR9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q969J2.1 GenPept UniProtKB/Swiss-Prot:Q969J2

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