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

Gene ID: 223752, updated on 7-Apr-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 and membrane. Predicted to be integral component of 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, Apr 2022]
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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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
acts_upstream_of_or_within apoptotic process IEA
Inferred from Electronic Annotation
more info
  
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 involved in apoptotic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in 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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