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    ZXDC ZXD family zinc finger C [ Homo sapiens (human) ]

    Gene ID: 79364, updated on 28-Oct-2024

    Summary

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    Official Symbol
    ZXDCprovided by HGNC
    Official Full Name
    ZXD family zinc finger Cprovided by HGNC
    Primary source
    HGNC:HGNC:28160
    See related
    Ensembl:ENSG00000070476 MIM:615746; AllianceGenome:HGNC:28160
    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
    ZXDL
    Summary
    Enables C2H2 zinc finger domain binding activity; LRR domain binding activity; and transcription coactivator activity. Involved in positive regulation of DNA-templated transcription. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 13.7), spleen (RPKM 5.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZXDC in Genome Data Viewer
    Location:
    3q21.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (126437601..126475891, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (129170156..129208446, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (126156444..126194734, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126116648-126117157 Neighboring gene CFAP100 divergent transcript Neighboring gene cilia and flagella associated protein 100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126127425-126127925 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126136999-126137896 Neighboring gene uncharacterized LOC124906280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126160086-126160721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126167171-126168110 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126186579-126187556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126193081-126193606 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14677 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14678 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:126204897-126205832 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:126207907-126209106 Neighboring gene urocanate hydratase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126216345-126217222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126229039-126229961 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:126239356-126239555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126242322-126242822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126242823-126243323 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126243384-126243884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126243885-126244385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:126248434-126249422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20439 Neighboring gene carbohydrate sulfotransferase 13 Neighboring gene chromosome 3 open reading frame 22 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:126258788-126258962

    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. An N- and C-terminal truncated isoform of zinc finger X-linked duplicated C protein represses MHC class II transcription. Aleksandrova A, et al. Mol Cell Biochem, 2010 Apr. PMID 19777325, Free PMC Article
    2. An eQTL variant of ZXDC is associated with IFN-γ production following Mycobacterium tuberculosis antigen-specific stimulation. Jabot-Hanin F, et al. Sci Rep, 2017 Oct 9. PMID 28993696, Free PMC Article
    3. The zinc finger transcription factor ZXDC activates CCL2 gene expression by opposing BCL6-mediated repression. Ramsey JE, et al. Mol Immunol, 2013 Dec. PMID 23954399, Free PMC Article
    4. CircZXDC Promotes Vascular Smooth Muscle Cell Transdifferentiation via Regulating miRNA-125a-3p/ABCC6 in Moyamoya Disease. Liu Y, et al. Cells, 2022 Nov 26. PMID 36497052, Free PMC Article
    5. ZXDC, a novel zinc finger protein that binds CIITA and activates MHC gene transcription. Al-Kandari W, et al. Mol Immunol, 2007 Jan. PMID 16600381, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CircZXDC Promotes Vascular Smooth Muscle Cell Transdifferentiation via Regulating miRNA-125a-3p/ABCC6 in Moyamoya Disease.
      Title: CircZXDC Promotes Vascular Smooth Muscle Cell Transdifferentiation via Regulating miRNA-125a-3p/ABCC6 in Moyamoya Disease.
    2. an expression quantitative trait loci of the ZXDC gene is associated with IFN-gamma production following Mycobacterium tuberculosis antigen-specific stimulation.
      Title: An eQTL variant of ZXDC is associated with IFN-γ production following Mycobacterium tuberculosis antigen-specific stimulation.
    3. Data show that ZXDC1 is a regulator in the process of myeloid function and that ZXDC1 is responsible for Ccl2 gene de-repression by BCL6.
      Title: The zinc finger transcription factor ZXDC activates CCL2 gene expression by opposing BCL6-mediated repression.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. Role of ZXD proteins in regulating MHC II transcription.
      Title: An N- and C-terminal truncated isoform of zinc finger X-linked duplicated C protein represses MHC class II transcription.
    6. study found sumoylation does not appear to disrupt or modulate interaction of ZXDC with binding partners; sumoylation of ZXDC is required for full activity of transcriptional activation domain; study suggests sumoylation is an important regulator of ZXDC
      Title: Sumoylation of the zinc finger protein ZXDC enhances the function of its transcriptional activation domain.
    7. ZXDA and ZXDC form an important regulatory complex for MHC II gene transcription.
      Title: The zinc finger proteins ZXDA and ZXDC form a complex that binds CIITA and regulates MHC II gene transcription.
    8. ZXDC is an important regulator of both MHC class I and class II transcription
      Title: ZXDC, a novel zinc finger protein that binds CIITA and activates MHC gene transcription.
    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

    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

    • FLJ13861, FLJ36477, FLJ37830, MGC11349, DKFZp547N024

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables C2H2 zinc finger domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables LRR domain 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 
    enables transcription coactivator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    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
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein ZXDC
    Names
    SERH2790
    ZXD-like zinc finger protein

    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_001040653.4 → NP_001035743.1  zinc finger protein ZXDC isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC024558, AF131763, BC110644, BM686637, CB268797, DQ079590, FJ980275
      Consensus CDS
      CCDS43146.1
      UniProtKB/Swiss-Prot
      Q2QGD7
      Related
      ENSP00000337694.5, ENST00000336332.5
      Conserved Domains (3) summary
      COG5048
      Location:284 → 443
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:333 → 352
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam17017
      Location:208 → 353
      zf-C2H2_aberr; Aberrant zinc-finger

    2. NM_025112.5 → NP_079388.3  zinc finger protein ZXDC isoform 1

      See identical proteins and their annotated locations for NP_079388.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC024558, DQ079590
      Consensus CDS
      CCDS43145.1
      UniProtKB/Swiss-Prot
      C5J0H9, Q2QGD7, Q6DKI8, Q7L3L1, Q8NAU2
      Related
      ENSP00000374359.3, ENST00000389709.8
      Conserved Domains (5) summary
      COG5048
      Location:284 → 443
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:333 → 352
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:208 → 232
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:375 → 401
      zf-H2C2_2; Zinc-finger double domain
      pfam17017
      Location:208 → 353
      zf-C2H2_aberr; Aberrant zinc-finger

    RNA

    1. NR_104249.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an internal exon and uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC024558, AL390142, BC063713, DQ079590, FJ980275

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      126437601..126475891 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011513119.3 → XP_011511421.1  zinc finger protein ZXDC isoform X1

      Conserved Domains (5) summary
      sd00017
      Location:333 → 352
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:208 → 232
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:375 → 401
      zf-H2C2_2; Zinc-finger double domain
      pfam15909
      Location:330 → 408
      zf-C2H2_8; C2H2-type zinc ribbon
      pfam17017
      Location:208 → 353
      zf-C2H2_aberr; Aberrant zinc-finger

    2. XM_006713741.3 → XP_006713804.1  zinc finger protein ZXDC isoform X2

      Conserved Domains (5) summary
      COG5048
      Location:284 → 443
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:333 → 352
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:208 → 232
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:375 → 401
      zf-H2C2_2; Zinc-finger double domain
      pfam17017
      Location:208 → 353
      zf-C2H2_aberr; Aberrant zinc-finger

    3. XM_005247757.4 → XP_005247814.1  zinc finger protein ZXDC isoform X3

      Conserved Domains (4) summary
      COG5048
      Location:284 → 443
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:333 → 352
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:375 → 401
      zf-H2C2_2; Zinc-finger double domain
      pfam17017
      Location:208 → 353
      zf-C2H2_aberr; Aberrant zinc-finger

    4. XM_047448901.1 → XP_047304857.1  zinc finger protein ZXDC isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      129170156..129208446 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347837.1 → XP_054203812.1  zinc finger protein ZXDC isoform X1

    2. XM_054347838.1 → XP_054203813.1  zinc finger protein ZXDC isoform X2

    3. XM_054347839.1 → XP_054203814.1  zinc finger protein ZXDC isoform X3

    4. XM_054347840.1 → XP_054203815.1  zinc finger protein ZXDC isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q2QGD7.2 GenPept UniProtKB/Swiss-Prot:Q2QGD7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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