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    Gramd4 GRAM domain containing 4 [ Mus musculus (house mouse) ]

    Gene ID: 223752, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Gramd4provided by MGI
    Official Full Name
    GRAM domain containing 4provided by MGI
    Primary source
    MGI:MGI:2676308
    See related
    Ensembl:ENSMUSG00000035900 AllianceGenome:MGI:2676308
    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
    9930016O13
    Summary
    Involved in negative regulation of toll-like receptor 9 signaling pathway. Predicted to be located in endoplasmic reticulum membrane and mitochondrial membrane. Predicted to be active in mitochondrion. Is expressed in central nervous system; dorsal root ganglion; and retina. Orthologous to human GRAMD4 (GRAM domain containing 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in whole brain E14.5 (RPKM 10.5), CNS E18 (RPKM 10.3) and 27 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Gramd4 in Genome Data Viewer
    Location:
    15 E2; 15 40.48 cM
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (85941896..86021837)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (86057695..86137636)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene cadherin, EGF LAG seven-pass G-type receptor 1 Neighboring gene STARR-seq mESC enhancer starr_39409 Neighboring gene predicted gene, 34764 Neighboring gene STARR-seq mESC enhancer starr_39412 Neighboring gene predicted gene, 41375 Neighboring gene STARR-positive B cell enhancer ABC_E9422 Neighboring gene predicted gene 15722 Neighboring gene STARR-positive B cell enhancer mm9_chr15:86003680-86003981 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:86012285-86012732 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:86013160-86013361 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:86033071-86033180 Neighboring gene ceramide kinase Neighboring gene predicted gene 15569 Neighboring gene TBC1 domain family, member 22a Neighboring gene predicted gene, 22818

    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. Endoplasmic Protein Nogo-B (RTN4-B) Interacts with GRAMD4 and Regulates TLR9-Mediated Innate Immune Responses. Kimura T, et al. J Immunol, 2015 Jun 1. PMID 25917084
    2. Phospho-proteomic analyses of B-Raf protein complexes reveal new regulatory principles. Eisenhardt AE, et al. Oncotarget, 2016 May 3. PMID 27034005, Free PMC Article
    3. Decreased expression levels of Ifi genes is associated to the increased resistance to spontaneous arthritis disease in mice deficiency of IL-1RA. Liu X, et al. BMC Immunol, 2016 Aug 2. PMID 27480124, Free PMC Article
    4. Inactivation of the microRNA-183/96/182 cluster results in syndromic retinal degeneration. Lumayag S, et al. Proc Natl Acad Sci U S A, 2013 Feb 5. PMID 23341629, Free PMC Article
    5. Prediction of the coding sequences of mouse homologues of KIAA gene: III. the complete nucleotide sequences of 500 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 Aug 31. PMID 14621295

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The findings indicate a critical role of Nogo-B and GRAMD4 in trafficking of TLR9.
      Title: Endoplasmic Protein Nogo-B (RTN4-B) Interacts with GRAMD4 and Regulates TLR9-Mediated Innate Immune Responses.
    Submit: New GeneRIF Correction

    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

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of toll-like receptor 9 signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of toll-like receptor 9 signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of cysteine-type endopeptidase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrial membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    GRAM domain-containing protein 4
    Names
    death-inducing 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_001205353.1 → NP_001192282.1  GRAM domain-containing protein 4 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, initiates translation at an alternate start codon, and uses an alternate splice site in the 3' coding region, compared to variant 1, which results in a translational frameshift. The encoded isoform (2) is shorter and has distinct N- and C-termini, compared to isoform 1.
      Source sequence(s)
      AC116764, BC085148
      Consensus CDS
      CCDS56998.1
      UniProtKB/TrEMBL
      D3YUE7, Q5U4C7
      Related
      ENSMUSP00000120796.2, ENSMUST00000138134.8
      Conserved Domains (2) summary
      cd13221
      Location:490 → 593
      PH-GRAM_GRAMDC4; GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam08372
      Location:335 → 427
      PRT_C; Plant phosphoribosyltransferase C-terminal

    2. NM_001379572.1 → NP_001366501.1  GRAM domain-containing protein 4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC116764
      UniProtKB/Swiss-Prot
      B2RTC1, Q6ZQ52, Q8CB44, Q8VDL6
      Conserved Domains (1) summary
      cd13221
      Location:490 → 595
      PH-GRAM_GRAMDC4; GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    3. NM_172611.5 → NP_766199.2  GRAM domain-containing protein 4 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).
      Source sequence(s)
      AC116764
      UniProtKB/Swiss-Prot
      B2RTC1, Q6ZQ52, Q8CB44, Q8VDL6
      Related
      ENSMUSP00000086321.4, ENSMUST00000088931.10
      Conserved Domains (3) summary
      cd13221
      Location:464 → 569
      PH-GRAM_GRAMDC4; GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam09755
      Location:37 → 130
      DUF2046; Uncharacterized conserved protein H4 (DUF2046)
      pfam08372
      Location:309 → 401
      PRT_C; Plant phosphoribosyltransferase C-terminal

    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_000081.7 Reference GRCm39 C57BL/6J

      Range
      85941896..86021837
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006520821.2 → XP_006520884.2  GRAM domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      Q5U4C7
      Conserved Domains (2) summary
      cd13221
      Location:515 → 618
      PH-GRAM_GRAMDC4; GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16515
      Location:141 → 187
      HIP1_clath_bdg; Clathrin-binding domain of Huntingtin-interacting protein 1

    2. XM_006520828.2 → XP_006520891.1  GRAM domain-containing protein 4 isoform X3

      See identical proteins and their annotated locations for XP_006520891.1

      UniProtKB/TrEMBL
      Q5U4C7
      Conserved Domains (3) summary
      cd13221
      Location:464 → 567
      PH-GRAM_GRAMDC4; GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam09755
      Location:37 → 130
      DUF2046; Uncharacterized conserved protein H4 (DUF2046)
      pfam16515
      Location:90 → 136
      HIP1_clath_bdg; Clathrin-binding domain of Huntingtin-interacting protein 1

    3. XM_006520829.4 → XP_006520892.1  GRAM domain-containing protein 4 isoform X3

      See identical proteins and their annotated locations for XP_006520892.1

      UniProtKB/TrEMBL
      Q5U4C7
      Conserved Domains (3) summary
      cd13221
      Location:464 → 567
      PH-GRAM_GRAMDC4; GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam09755
      Location:37 → 130
      DUF2046; Uncharacterized conserved protein H4 (DUF2046)
      pfam16515
      Location:90 → 136
      HIP1_clath_bdg; Clathrin-binding domain of Huntingtin-interacting protein 1

    4. XM_006520822.4 → XP_006520885.1  GRAM domain-containing protein 4 isoform X2

      UniProtKB/TrEMBL
      Q5U4C7
      Conserved Domains (2) summary
      cd13221
      Location:517 → 620
      PH-GRAM_GRAMDC4; GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam16515
      Location:143 → 189
      HIP1_clath_bdg; Clathrin-binding domain of Huntingtin-interacting protein 1

    RNA

    1. XR_003951368.1 RNA Sequence

      Related
      ENSMUST00000123349.2
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8CB44.1 GenPept UniProtKB/Swiss-Prot:Q8CB44

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