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Zdbf2 zinc finger, DBF-type containing 2 [ Mus musculus (house mouse) ]

Gene ID: 73884, updated on 11-Apr-2024

Summary

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Official Symbol
Zdbf2provided by MGI
Official Full Name
zinc finger, DBF-type containing 2provided by MGI
Primary source
MGI:MGI:1921134
See related
Ensembl:ENSMUSG00000027520 AllianceGenome:MGI:1921134
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
4930431J08Rik; 9330107J05Rik
Summary
Acts upstream of or within DNA methylation involved in embryo development and genetic imprinting. Is expressed in several structures, including alimentary system; brain; early conceptus; genitourinary system; and limb segment. Orthologous to human ZDBF2 (zinc finger DBF-type containing 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis adult (RPKM 4.5), whole brain E14.5 (RPKM 4.2) and 8 other tissues See more
Orthologs
human all
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Genomic context

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Location:
1; 1 C2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (63239517..63353735)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (63200358..63314576)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E3279 Neighboring gene predicted gene, 26457 Neighboring gene small nucleolar RNA, H/ACA box 41 Neighboring gene eukaryotic translation elongation factor 1 beta 2 Neighboring gene STARR-seq mESC enhancer starr_01131 Neighboring gene chemerin chemokine-like receptor 2 Neighboring gene STARR-seq mESC enhancer starr_01132 Neighboring gene STARR-seq mESC enhancer starr_01135 Neighboring gene RIKEN cDNA 1700039I01 gene Neighboring gene STARR-seq mESC enhancer starr_01137 Neighboring gene predicted gene 11608 Neighboring gene predicted gene, 23448 Neighboring gene STARR-seq mESC enhancer starr_01138 Neighboring gene pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3 pseudogene Neighboring gene PRELI domain containing 1 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Guttman M, et al. Nat Biotechnol, 2010 May. PMID 20436462, 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. Transient transcription in the early embryo sets an epigenetic state that programs postnatal growth. Greenberg MV, et al. Nat Genet, 2017 Jan. PMID 27841881
  5. Imprinted DNA methylation reprogramming during early mouse embryogenesis at the Gpr1-Zdbf2 locus is linked to long cis-intergenic transcription. Kobayashi H, et al. FEBS Lett, 2012 Mar 23. PMID 22449967

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The imprinted Zdbf2 gene finely tunes control of feeding and growth in neonates.
    Title: The imprinted Zdbf2 gene finely tunes control of feeding and growth in neonates.
  2. a maternal germline differentially methylated region (DMR) at the mouse Gpr1/Zdbf2 (DBF-type zinc finger-containing protein 2) locus, which controls the paternal-specific expression of long isoforms of Zdbf2 (Liz) in the early embryo
    Title: The Gpr1/Zdbf2 locus provides new paradigms for transient and dynamic genomic imprinting in mammals.
  3. Results identified a novel, paternally expressed, long intergenic non-coding Zdbf2 variant (Zdbf2linc) transcribed from maternally methylated Gpr1 during early embryogenesis in the mouse.
    Title: Imprinted DNA methylation reprogramming during early mouse embryogenesis at the Gpr1-Zdbf2 locus is linked to long cis-intergenic transcription.
  4. Identification of differentially methylated regions within the Gpr1-Zdbf2 imprinted domain.
    Title: A tripartite paternally methylated region within the Gpr1-Zdbf2 imprinted domain on mouse chromosome 1 identified by meDIP-on-chip.
  5. Zdbf2 was paternally expressed in various embryonic and adult tissues, except for the placenta and adult testis, which showed biallelic expression of the gene.
    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

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (1) 
  • Endonuclease-mediated (6)  1 citation

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in epigenetic programming of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within epigenetic programming of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in genomic imprinting IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within genomic imprinting IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  

General protein information

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Preferred Names
DBF4-type zinc finger-containing protein 2 homolog

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_001267872.1 → NP_001254801.1  DBF4-type zinc finger-containing protein 2 homolog isoform 1

    See identical proteins and their annotated locations for NP_001254801.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AK015271, AK132808, AL669947
    Consensus CDS
    CCDS48278.1
    UniProtKB/Swiss-Prot
    Q3V0Y4, Q5SS00, Q9CUN4
    Conserved Domains (2) summary
    pfam15042
    Location:2276 → 2330
    LELP1; Late cornified envelope-like proline-rich protein 1
    NF033845
    Location:655 → 875
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

  2. NM_001285936.1 → NP_001272865.1  DBF4-type zinc finger-containing protein 2 homolog isoform 2

    See identical proteins and their annotated locations for NP_001272865.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate promoter, contains several novel exons, lacks few exons, and initiates translation from an alternate start codon compared to variant 1. The resulting longer isoform (2) has a distinct N-terminus compared to isoform 1. Variants 3 and 4 encode the same isoform. Note, this variant has been described as long intergenic non-coding Zdbf2 variant (Zdbf2linc) transcribed from a maternally methylated region during early embryogenesis in mouse (PMID:22449967).
    Source sequence(s)
    AB777270
    UniProtKB/TrEMBL
    A0A6I8MWW6
    Conserved Domains (3) summary
    pfam15042
    Location:2281 → 2335
    LELP1; Late cornified envelope-like proline-rich protein 1
    NF033845
    Location:660 → 880
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
    cl02684
    Location:3 → 34
    zf-DBF; DBF zinc finger

  3. NM_001285937.1 → NP_001272866.1  DBF4-type zinc finger-containing protein 2 homolog isoform 2

    See identical proteins and their annotated locations for NP_001272866.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate promoter, contains several novel exons, lacks few exons, and initiates translation from an alternate start codon compared to variant 1. The resulting longer isoform (2) has a distinct N-terminus compared to isoform 1. Variants 3 and 4 encode the same isoform.
    Source sequence(s)
    AB777269, AB777270
    UniProtKB/TrEMBL
    A0A6I8MWW6
    Conserved Domains (3) summary
    pfam15042
    Location:2281 → 2335
    LELP1; Late cornified envelope-like proline-rich protein 1
    NF033845
    Location:660 → 880
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
    cl02684
    Location:3 → 34
    zf-DBF; DBF zinc finger

  4. NM_028673.1 → NP_082949.1  DBF4-type zinc finger-containing protein 2 homolog isoform 1

    See identical proteins and their annotated locations for NP_082949.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the shorter isoform (1). Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AK015271, AL669947
    Consensus CDS
    CCDS48278.1
    UniProtKB/Swiss-Prot
    Q3V0Y4, Q5SS00, Q9CUN4
    Related
    ENSMUSP00000109767.2, ENSMUST00000114132.8
    Conserved Domains (2) summary
    pfam15042
    Location:2276 → 2330
    LELP1; Late cornified envelope-like proline-rich protein 1
    NF033845
    Location:655 → 875
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000067.7 Reference GRCm39 C57BL/6J

    Range
    63239517..63353735
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011238607.4 → XP_011236909.1  DBF4-type zinc finger-containing protein 2 homolog isoform X1

    See identical proteins and their annotated locations for XP_011236909.1

    UniProtKB/TrEMBL
    A0A6I8MWW6
    Conserved Domains (3) summary
    pfam15042
    Location:2281 → 2335
    LELP1; Late cornified envelope-like proline-rich protein 1
    NF033845
    Location:660 → 880
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
    cl02684
    Location:3 → 34
    zf-DBF; DBF zinc finger

  2. XM_030243195.1 → XP_030099055.1  DBF4-type zinc finger-containing protein 2 homolog isoform X2

    UniProtKB/Swiss-Prot
    Q3V0Y4, Q5SS00, Q9CUN4
    Conserved Domains (2) summary
    pfam15042
    Location:2276 → 2330
    LELP1; Late cornified envelope-like proline-rich protein 1
    NF033845
    Location:655 → 875
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

  3. XM_036153851.1 → XP_036009744.1  DBF4-type zinc finger-containing protein 2 homolog isoform X2

    UniProtKB/Swiss-Prot
    Q3V0Y4, Q5SS00, Q9CUN4
    Related
    ENSMUSP00000029025.9, ENSMUST00000029025.9
    Conserved Domains (2) summary
    pfam15042
    Location:2276 → 2330
    LELP1; Late cornified envelope-like proline-rich protein 1
    NF033845
    Location:655 → 875
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

  4. XM_030243197.1 → XP_030099057.1  DBF4-type zinc finger-containing protein 2 homolog isoform X3

    Conserved Domains (1) summary
    pfam15042
    Location:1474 → 1526
    LELP1; Late cornified envelope-like proline-rich protein 1

  5. XM_030243194.1 → XP_030099054.1  DBF4-type zinc finger-containing protein 2 homolog isoform X2

    UniProtKB/Swiss-Prot
    Q3V0Y4, Q5SS00, Q9CUN4
    Conserved Domains (2) summary
    pfam15042
    Location:2276 → 2330
    LELP1; Late cornified envelope-like proline-rich protein 1
    NF033845
    Location:655 → 875
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

  6. XM_011238606.3 → XP_011236908.1  DBF4-type zinc finger-containing protein 2 homolog isoform X1

    See identical proteins and their annotated locations for XP_011236908.1

    UniProtKB/TrEMBL
    A0A6I8MWW6
    Related
    ENSMUSP00000159296.2, ENSMUST00000239483.2
    Conserved Domains (3) summary
    pfam15042
    Location:2281 → 2335
    LELP1; Late cornified envelope-like proline-rich protein 1
    NF033845
    Location:660 → 880
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
    cl02684
    Location:3 → 34
    zf-DBF; DBF zinc finger

  7. XM_030243196.1 → XP_030099056.1  DBF4-type zinc finger-containing protein 2 homolog isoform X2

    UniProtKB/Swiss-Prot
    Q3V0Y4, Q5SS00, Q9CUN4
    Conserved Domains (2) summary
    pfam15042
    Location:2276 → 2330
    LELP1; Late cornified envelope-like proline-rich protein 1
    NF033845
    Location:655 → 875
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

  8. XM_036153849.1 → XP_036009742.1  DBF4-type zinc finger-containing protein 2 homolog isoform X1

    UniProtKB/TrEMBL
    A0A6I8MWW6
    Conserved Domains (3) summary
    pfam15042
    Location:2281 → 2335
    LELP1; Late cornified envelope-like proline-rich protein 1
    NF033845
    Location:660 → 880
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
    cl02684
    Location:3 → 34
    zf-DBF; DBF zinc finger

  9. XM_036153852.1 → XP_036009745.1  DBF4-type zinc finger-containing protein 2 homolog isoform X2

    UniProtKB/Swiss-Prot
    Q3V0Y4, Q5SS00, Q9CUN4
    Conserved Domains (2) summary
    pfam15042
    Location:2276 → 2330
    LELP1; Late cornified envelope-like proline-rich protein 1
    NF033845
    Location:655 → 875
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5SS00.1 GenPept UniProtKB/Swiss-Prot:Q5SS00

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