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

Gene ID: 76510, updated on 2-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 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

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