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    Trappc9 trafficking protein particle complex 9 [ Mus musculus (house mouse) ]

    Gene ID: 76510, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Trappc9provided by MGI
    Official Full Name
    trafficking protein particle complex 9provided by MGI
    Primary source
    MGI:MGI:1923760
    See related
    Ensembl:ENSMUSG00000047921 AllianceGenome:MGI:1923760
    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
    Ibp; Nibp; TRS130; mKIAA1882; 1810044A24Rik; 2900005P22Rik; 4632408O18Rik
    Summary
    Acts upstream of or within neuron differentiation and positive regulation of NF-kappaB transcription factor activity. Located in cytoplasm. Is expressed in brain. Used to study intellectual disability. Human ortholog(s) of this gene implicated in autosomal recessive intellectual developmental disorder 13. Orthologous to human TRAPPC9 (trafficking protein particle complex subunit 9). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in adrenal adult (RPKM 14.2), genital fat pad adult (RPKM 11.4) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Trappc9 in Genome Data Viewer
    Location:
    15 D3; 15 33.7 cM
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (72461469..72933086, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (72589620..73061238, complement)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 24390 Neighboring gene STARR-positive B cell enhancer ABC_E8594 Neighboring gene potassium channel, subfamily K, member 9 Neighboring gene STARR-seq mESC enhancer starr_38933 Neighboring gene STARR-seq mESC enhancer starr_38934 Neighboring gene predicted gene, 28020 Neighboring gene predicted gene, 53896 Neighboring gene STARR-positive B cell enhancer ABC_E10860 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:72695941-72696136 Neighboring gene paternally expressed 13 Neighboring gene predicted gene, 41343 Neighboring gene predicted gene, 53258 Neighboring gene STARR-seq mESC enhancer starr_38939 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:72759279-72759495 Neighboring gene STARR-seq mESC enhancer starr_38940 Neighboring gene guanine nucleotide binding protein (G protein), gamma 5 pseudogene Neighboring gene STARR-seq mESC enhancer starr_38942 Neighboring gene predicted gene, 31665 Neighboring gene VISTA enhancer mm1679 Neighboring gene STARR-positive B cell enhancer ABC_E1908 Neighboring gene STARR-positive B cell enhancer ABC_E1479 Neighboring gene STARR-positive B cell enhancer ABC_E7378 Neighboring gene STARR-seq mESC enhancer starr_38946 Neighboring gene chromatin accessibility complex 1 Neighboring gene predicted gene, 31725 Neighboring gene argonaute RISC catalytic subunit 2

    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. Microcephaly with a disproportionate hippocampal reduction, stem cell loss and neuronal lipid droplet symptoms in Trappc9 KO mice. Aljuraysi S, et al. Neurobiol Dis, 2024 Mar. PMID 38331351
    2. Trappc9 Deficiency Impairs the Plasticity of Stem Cells. Usman M, et al. Int J Mol Sci, 2022 Apr 28. PMID 35563289, Free PMC Article
    3. Trappc9 deficiency in mice impairs learning and memory by causing imbalance of dopamine D1 and D2 neurons. Ke Y, et al. Sci Adv, 2020 Nov. PMID 33208359, Free PMC Article
    4. Loss of IRF-4-binding protein leads to the spontaneous development of systemic autoimmunity. Fanzo JC, et al. J Clin Invest, 2006 Mar. PMID 16470246, Free PMC Article
    5. Expression and function of NIK- and IKK2-binding protein (NIBP) in mouse enteric nervous system. Zhang Y, et al. Neurogastroenterol Motil, 2014 Jan. PMID 24011459, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Microcephaly with a disproportionate hippocampal reduction, stem cell loss and neuronal lipid droplet symptoms in Trappc9 KO mice.
      Title: Microcephaly with a disproportionate hippocampal reduction, stem cell loss and neuronal lipid droplet symptoms in Trappc9 KO mice.
    2. Defective neurite elongation and branching in Nibp/Trappc9 deficient zebrafish and mice.
      Title: Defective neurite elongation and branching in Nibp/Trappc9 deficient zebrafish and mice.
    3. A novel regulatory role of TRAPPC9 in L-plastin-mediated osteoclast actin ring formation.
      Title: A novel regulatory role of TRAPPC9 in L-plastin-mediated osteoclast actin ring formation.
    4. NIBP is extensively expressed in the enteric nervous system with relatively high level in a subpopulation of enteric neurons.
      Title: Expression and function of NIK- and IKK2-binding protein (NIBP) in mouse enteric nervous system.
    5. Data show Trs130 (mTrs130) is a component of an analogous TRAPP complex that this complex is enriched on COPI (Coat Protein I)-coated vesicles it specifically activates Rab1.
      Title: mTrs130 is a component of a mammalian TRAPPII complex, a Rab1 GEF that binds to COPI-coated vesicles.
    6. TRAPPC9 has a role in brain development, possibly through its effect on NF-kappaB activation and protein trafficking in the postmitotic neurons of the cerebral cortex
      Title: A truncating mutation of TRAPPC9 is associated with autosomal-recessive intellectual disability and postnatal microcephaly.
    7. IBP, a novel regulator of Rho GTPases, is required for optimal T cell effector function, lymphocyte homeostasis, and the prevention of systemic autoimmunity.
      Title: Loss of IRF-4-binding protein leads to the spontaneous development of systemic autoimmunity.
    8. NIBP is a NIK and IKK(beta)-binding protein that enhances NF-(kappa)B activation.
      Title: NIBP, a novel NIK and IKK(beta)-binding protein that enhances NF-(kappa)B activation.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (3)  1 citation
    • Gene trapped (2) 
    • Targeted (2) 

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1882

    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 cerebral cortex development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of NF-kappaB transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vesicle coating NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in vesicle tethering NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    NOT located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of TRAPP complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of TRAPPII protein complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    NOT located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    NOT located_in late endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    trafficking protein particle complex subunit 9
    Names
    Ikk2 binding protein
    NIK and IKK(beta) binding protein
    NIK- and IKBKB-binding 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_001164641.1 → NP_001158113.1  trafficking protein particle complex subunit 9 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an exon in the coding region, which results in a frameshift and an early stop codon, compared to variant 2. The encoded isoform (3) has a distinct C-terminus, compared to isoform 2.
      Source sequence(s)
      AK029106, BC070463
      Consensus CDS
      CCDS49630.1
      UniProtKB/TrEMBL
      E9Q3T8
      Related
      ENSMUSP00000131997.2, ENSMUST00000170633.9
      Conserved Domains (1) summary
      pfam08626
      Location:70 → 795
      TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

    2. NM_001164643.1 → NP_001158115.1  trafficking protein particle complex subunit 9 isoform 5

      See identical proteins and their annotated locations for NP_001158115.1

      Status: VALIDATED

      Description
      Transcript Variant: Transcript Variant: This variant (5) lacks an exon in the coding region, which results in a frameshift and an early stop codon, compared to variant 2. The encoded isoform (5) has a distinct C-terminus, compared to isoform 2.
      Source sequence(s)
      AC118234, AK031788, BC070463
      Consensus CDS
      CCDS88775.1
      UniProtKB/Swiss-Prot
      Q3U0M1
      Related
      ENSMUSP00000155105.2, ENSMUST00000228960.2
      Conserved Domains (1) summary
      pfam08626
      Location:70 → 494
      TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

    3. NM_029640.2 → NP_083916.1  trafficking protein particle complex subunit 9 isoform 1

      See identical proteins and their annotated locations for NP_083916.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 2. The encoded isoform (1) has a distinct N-terminus and is shorter than isoform 2.
      Source sequence(s)
      AC118640, BC034590
      Consensus CDS
      CCDS37096.1
      UniProtKB/Swiss-Prot
      Q3U0M1
      Related
      ENSMUSP00000023276.9, ENSMUST00000023276.16
      Conserved Domains (1) summary
      pfam08626
      Location:10 → 914
      TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

    4. NM_180662.2 → NP_850993.2  trafficking protein particle complex subunit 9 isoform 2

      See identical proteins and their annotated locations for NP_850993.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).
      Source sequence(s)
      AY630620, BC070463
      Consensus CDS
      CCDS37095.1
      UniProtKB/Swiss-Prot
      Q3U0M1
      Related
      ENSMUSP00000087202.4, ENSMUST00000089770.11
      Conserved Domains (1) summary
      pfam08626
      Location:70 → 1093
      TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

    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
      72461469..72933086 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006521527.5 → XP_006521590.1  trafficking protein particle complex subunit 9 isoform X1

      See identical proteins and their annotated locations for XP_006521590.1

      UniProtKB/Swiss-Prot
      Q3U0M1, Q3UU81, Q69Z79, Q6NS50, Q8CD01, Q8CFV8, Q9D8R6
      Conserved Domains (1) summary
      pfam08626
      Location:70 → 1102
      TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

    2. XM_017316788.2 → XP_017172277.1  trafficking protein particle complex subunit 9 isoform X2

      Conserved Domains (1) summary
      pfam08626
      Location:10 → 905
      TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

    RNA

    1. XR_001781576.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001164642.1: Suppressed sequence

      Description
      NM_001164642.1: This RefSeq was removed because currently there is insufficient support for the 3' end of the transcript.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3U0M1.2 GenPept UniProtKB/Swiss-Prot:Q3U0M1

    Gene LinkOut

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

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