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ZDBF2 zinc finger DBF-type containing 2 [ Homo sapiens (human) ]

Gene ID: 57683, updated on 11-Apr-2024

Summary

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Official Symbol
ZDBF2provided by HGNC
Official Full Name
zinc finger DBF-type containing 2provided by HGNC
Primary source
HGNC:HGNC:29313
See related
Ensembl:ENSG00000204186 MIM:617059; AllianceGenome:HGNC:29313
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Slx9
Summary
This gene encodes a protein containing DBF4-type zinc finger domains. This gene is imprinted and paternally expressed in lymphocytes but is more stochastically expressed in the placenta. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2015]
Expression
Ubiquitous expression in adrenal (RPKM 4.6), brain (RPKM 4.3) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See ZDBF2 in Genome Data Viewer
Location:
2q33.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (206274663..206314427)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (206756581..206796353)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (207139387..207179151)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene CMKLR2 antisense RNA Neighboring gene RN7SK pseudogene 260 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12267 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:207139745-207140244 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:207192998-207193988 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:207193989-207194978 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:207232447-207232644 Neighboring gene Sharpr-MPRA regulatory region 7385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:207280066-207280566 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 51 Neighboring gene ACER2 pseudogene 1

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. Exome sequencing identifies a de novo frameshift mutation in the imprinted gene ZDBF2 in a sporadic patient with Nasopalpebral Lipoma-coloboma syndrome. Chacón-Camacho OF, et al. Am J Med Genet A, 2016 Jul. PMID 27139419, Free PMC Article
  2. Identification of the mouse paternally expressed imprinted gene Zdbf2 on chromosome 1 and its imprinted human homolog ZDBF2 on chromosome 2. Kobayashi H, et al. Genomics, 2009 May. PMID 19200453
  3. Epigenetic and transcriptional features of the novel human imprinted lncRNA GPR1AS suggest it is a functional ortholog to mouse Zdbf2linc. Kobayashi H, et al. Epigenetics, 2013 Jun. PMID 23764515, Free PMC Article
  4. Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder. Bergen SE, et al. Mol Psychiatry, 2012 Sep. PMID 22688191, Free PMC Article
  5. Protein phosphatase 1γ isoforms linked interactions in the brain. Esteves SL, et al. J Mol Neurosci, 2013 May. PMID 23080069

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Exome sequencing identified a de novo heterozygous frameshift dinucleotide insertion c.6245_6246 insTT (p.His2082fs*67) in ZDBF2 (zinc finger, DBF-type containing 2), a gene located at 2q33.3. This variant was absent in parental DNA, in a set of 300 ethnically matched controls, and in public exome variant databases
    Title: Exome sequencing identifies a de novo frameshift mutation in the imprinted gene ZDBF2 in a sporadic patient with Nasopalpebral Lipoma-coloboma syndrome.
  2. the human homolog (ZDBF2) of the mouse Zdbf2 gene showed paternal allele-specific expression in human lymphocytes but not in the human placenta.
    Title: Identification of the mouse paternally expressed imprinted gene Zdbf2 on chromosome 1 and its imprinted human homolog ZDBF2 on chromosome 2.
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 in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder.
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

  • FLJ45338, KIAA1571

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in epigenetic programming of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in genomic imprinting IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
DBF4-type zinc finger-containing protein 2

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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.

Genomic

  1. NG_045219.1 RefSeqGene

    Range
    5023..44787
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1065

mRNA and Protein(s)

  1. NM_001285549.2 → NP_001272478.1  DBF4-type zinc finger-containing protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001272478.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon, two additional exons in the 5' region, and initiates translation from an alternate start codon compared to variant 1. The resulting shorter isoform (2) has a novel N-terminus compared to isoform 1.
    Source sequence(s)
    AB775780, AC017081, BQ021839
    UniProtKB/TrEMBL
    N0DVX5

  2. NM_001369654.1 → NP_001356583.1  DBF4-type zinc finger-containing protein 2 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC017081
    Consensus CDS
    CCDS46501.1
    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2
    Related
    ENSP00000497308.1, ENST00000649650.1
    Conserved Domains (1) summary
    cl02684
    Location:6 → 29
    zf-DBF; DBF zinc finger

  3. NM_020923.3 → NP_065974.1  DBF4-type zinc finger-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_065974.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AB775781, BQ021839
    Consensus CDS
    CCDS46501.1
    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2
    Related
    ENSP00000363545.3, ENST00000374423.9
    Conserved Domains (1) summary
    cl02684
    Location:6 → 29
    zf-DBF; DBF zinc finger

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    206274663..206314427
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047445282.1 → XP_047301238.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  2. XM_017004573.3 → XP_016860062.1  DBF4-type zinc finger-containing protein 2 isoform X2

    UniProtKB/TrEMBL
    N0DVX5

  3. XM_047445300.1 → XP_047301256.1  DBF4-type zinc finger-containing protein 2 isoform X2

    UniProtKB/TrEMBL
    N0DVX5

  4. XM_017004575.3 → XP_016860064.1  DBF4-type zinc finger-containing protein 2 isoform X3

    Conserved Domains (1) summary
    cl02684
    Location:6 → 29
    zf-DBF; DBF zinc finger

  5. XM_011511532.4 → XP_011509834.1  DBF4-type zinc finger-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011509834.1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2
    Conserved Domains (1) summary
    cl02684
    Location:6 → 29
    zf-DBF; DBF zinc finger

  6. XM_005246712.6 → XP_005246769.1  DBF4-type zinc finger-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_005246769.1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2
    Conserved Domains (1) summary
    cl02684
    Location:6 → 29
    zf-DBF; DBF zinc finger

  7. XM_047445281.1 → XP_047301237.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  8. XM_011511535.4 → XP_011509837.1  DBF4-type zinc finger-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011509837.1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2
    Conserved Domains (1) summary
    cl02684
    Location:6 → 29
    zf-DBF; DBF zinc finger

  9. XM_005246713.4 → XP_005246770.1  DBF4-type zinc finger-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_005246770.1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2
    Conserved Domains (1) summary
    cl02684
    Location:6 → 29
    zf-DBF; DBF zinc finger

  10. XM_011511533.3 → XP_011509835.1  DBF4-type zinc finger-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011509835.1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2
    Conserved Domains (1) summary
    cl02684
    Location:6 → 29
    zf-DBF; DBF zinc finger

  11. XM_011511534.3 → XP_011509836.1  DBF4-type zinc finger-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011509836.1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2
    Conserved Domains (1) summary
    cl02684
    Location:6 → 29
    zf-DBF; DBF zinc finger

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_015495299.1 Reference GRCh38.p14 PATCHES

    Range
    388301..428076
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331997.1 → XP_054187972.1  DBF4-type zinc finger-containing protein 2 isoform X3

  2. XM_054331990.1 → XP_054187965.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  3. XM_054331996.1 → XP_054187971.1  DBF4-type zinc finger-containing protein 2 isoform X2

    UniProtKB/TrEMBL
    N0DVX5

  4. XM_054331995.1 → XP_054187970.1  DBF4-type zinc finger-containing protein 2 isoform X2

    UniProtKB/TrEMBL
    N0DVX5

  5. XM_054331988.1 → XP_054187963.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  6. XM_054331993.1 → XP_054187968.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  7. XM_054331992.1 → XP_054187967.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  8. XM_054331994.1 → XP_054187969.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  9. XM_054331987.1 → XP_054187962.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  10. XM_054331989.1 → XP_054187964.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  11. XM_054331991.1 → XP_054187966.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    206756581..206796353
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054343224.1 → XP_054199199.1  DBF4-type zinc finger-containing protein 2 isoform X3

  2. XM_054343217.1 → XP_054199192.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  3. XM_054343223.1 → XP_054199198.1  DBF4-type zinc finger-containing protein 2 isoform X2

    UniProtKB/TrEMBL
    N0DVX5

  4. XM_054343222.1 → XP_054199197.1  DBF4-type zinc finger-containing protein 2 isoform X2

    UniProtKB/TrEMBL
    N0DVX5

  5. XM_054343215.1 → XP_054199190.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  6. XM_054343220.1 → XP_054199195.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  7. XM_054343219.1 → XP_054199194.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  8. XM_054343221.1 → XP_054199196.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  9. XM_054343214.1 → XP_054199189.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  10. XM_054343216.1 → XP_054199191.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2

  11. XM_054343218.1 → XP_054199193.1  DBF4-type zinc finger-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q6ZNP7, Q6ZSN8, Q9HCK1
    UniProtKB/TrEMBL
    N0DVB2
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9HCK1.3 GenPept UniProtKB/Swiss-Prot:Q9HCK1

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