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

    Gene ID: 73884, updated on 9-Dec-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 genomic 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, Dec 2024]
    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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    See Zdbf2 in Genome Data Viewer
    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)
    • Endonuclease-mediated (6)  1 citation
    • Targeted (1) 

    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
    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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