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    Dennd4b DENN domain containing 4B [ Mus musculus (house mouse) ]

    Gene ID: 229541, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Dennd4bprovided by MGI
    Official Full Name
    DENN domain containing 4Bprovided by MGI
    Primary source
    MGI:MGI:2446201
    See related
    Ensembl:ENSMUSG00000042404 AllianceGenome:MGI:2446201
    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
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of Rab protein signal transduction. Predicted to be located in Golgi apparatus and nucleoplasm. Predicted to be active in cytoplasmic vesicle. Orthologous to human DENND4B (DENN domain containing 4B). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in spleen adult (RPKM 39.3), thymus adult (RPKM 27.8) and 23 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Dennd4b in Genome Data Viewer
    Location:
    3 F1; 3 39.21 cM
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (90172281..90187972)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (90265020..90280665)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E1265 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:90052523-90052632 Neighboring gene cAMP responsive element binding protein 3-like 4 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:90057967-90058076 Neighboring gene solute carrier family 39 (zinc transporter), member 1 Neighboring gene STARR-positive B cell enhancer ABC_E4558 Neighboring gene CREB regulated transcription coactivator 2 Neighboring gene microRNA 7012 Neighboring gene STARR-positive B cell enhancer ABC_E28 Neighboring gene GATA zinc finger domain containing 2B Neighboring gene STARR-seq mESC enhancer starr_08281 Neighboring gene STARR-positive B cell enhancer ABC_E9009 Neighboring gene STARR-seq mESC enhancer starr_08284 Neighboring gene solute carrier family 27 (fatty acid transporter), member 3 Neighboring gene integrator complex subunit 3

    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. DENN domain proteins: regulators of Rab GTPases. Marat AL, et al. J Biol Chem, 2011 Apr 22. PMID 21330364, Free PMC Article
    2. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. Yoshimura S, et al. J Cell Biol, 2010 Oct 18. PMID 20937701, Free PMC Article
    3. Identification of new ciliary signaling pathways in the brain and insights into neurological disorders. Loukil A, et al. bioRxiv, 2023 Dec 21. PMID 38187761, Free PMC Article
    4. Prediction of the coding sequences of mouse homologues of KIAA gene: II. The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. Okazaki N, et al. DNA Res, 2003 Feb 28. PMID 12693553
    5. Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. Hansen GM, et al. Genome Res, 2008 Oct. PMID 18799693, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • mKIAA0476

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables guanyl-nucleotide exchange factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of Rab protein signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of Rab protein signal transduction ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in cytoplasmic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    DENN domain-containing protein 4B
    Names
    DENN/MADD domain containing 4B
    brain specific protein 4
    brain-specific gene 4 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_001356483.1 → NP_001343412.1  DENN domain-containing protein 4B isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC119825
      Consensus CDS
      CCDS89660.1
      UniProtKB/Swiss-Prot
      Q3U1Y4, Q6NZJ7, Q6R5M4, Q80TZ2, Q80VU7, Q8CGE6, Q8R0E9
      UniProtKB/TrEMBL
      B9EKY0
      Related
      ENSMUSP00000117354.2, ENSMUST00000129564.8
      Conserved Domains (5) summary
      smart00801
      Location:563 → 636
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:191 → 279
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:813 → 842
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:313 → 497
      DENN; DENN (AEX-3) domain
      pfam13041
      Location:811 → 851
      PPR_2; PPR repeat family

    2. NM_001405414.1 → NP_001392343.1  DENN domain-containing protein 4B isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC119825
      UniProtKB/Swiss-Prot
      Q3U1Y4, Q6NZJ7, Q6R5M4, Q80TZ2, Q80VU7, Q8CGE6, Q8R0E9

    3. NM_001405415.1 → NP_001392344.1  DENN domain-containing protein 4B isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC119825

    4. NM_201407.4 → NP_958809.3  DENN domain-containing protein 4B isoform 1

      See identical proteins and their annotated locations for NP_958809.3

      Status: VALIDATED

      Source sequence(s)
      AC119825, AK155638, BC066102
      Consensus CDS
      CCDS38502.2
      UniProtKB/TrEMBL
      A0A0R4J172, B9EKY0
      Related
      ENSMUSP00000096514.4, ENSMUST00000098914.10
      Conserved Domains (5) summary
      smart00801
      Location:574 → 647
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:202 → 290
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:824 → 853
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:324 → 508
      DENN; DENN (AEX-3) domain
      pfam13041
      Location:822 → 862
      PPR_2; PPR repeat family

    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_000069.7 Reference GRCm39 C57BL/6J

      Range
      90172281..90187972
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017319543.2 → XP_017175032.1  DENN domain-containing protein 4B isoform X1

      UniProtKB/TrEMBL
      B9EKY0
      Conserved Domains (5) summary
      smart00801
      Location:588 → 661
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:216 → 304
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:838 → 867
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:338 → 522
      DENN; DENN (AEX-3) domain
      pfam13041
      Location:836 → 876
      PPR_2; PPR repeat family

    2. XM_036163054.1 → XP_036018947.1  DENN domain-containing protein 4B isoform X4

      Conserved Domains (3) summary
      smart00801
      Location:1 → 63
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:240 → 269
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:238 → 278
      PPR_2; PPR repeat family

    RNA

    1. XR_375516.4 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3U1Y4.2 GenPept UniProtKB/Swiss-Prot:Q3U1Y4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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