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

    Gene ID: 57683, updated on 10-Dec-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
    NEW
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (206274663..206314427)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (206756581..206796353)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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 (34) 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)

    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 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_2024_08

    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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