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

Gene ID: 79364, updated on 5-Mar-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 transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 13.7), spleen (RPKM 5.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
3q21.3
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (126437601..126475891, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (129170156..129208446, complement)
105.20220307 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
  • 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 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
  2. 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
  3. 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
  4. 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
  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 (35) 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_2023_10

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

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