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TRAPPC9 trafficking protein particle complex 9 [ Homo sapiens (human) ]

Gene ID: 83696, updated on 17-Jun-2019

Summary

Official Symbol
TRAPPC9provided by HGNC
Official Full Name
trafficking protein particle complex 9provided by HGNC
Primary source
HGNC:HGNC:30832
See related
Ensembl:ENSG00000167632 MIM:611966
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
T1; IBP; NIBP; MRT13; TRS120; IKBKBBP
Summary
This gene encodes a protein that likely plays a role in NF-kappa-B signaling. Mutations in this gene have been associated with autosomal-recessive cognitive disability. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb 2010]
Expression
Ubiquitous expression in brain (RPKM 3.1), thyroid (RPKM 2.8) and 25 other tissues See more
Orthologs

Genomic context

See TRAPPC9 in Genome Data Viewer
Location:
8q24.3
Exon count:
29
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (139727725..140458579, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (140740324..141468678, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene potassium two pore domain channel subfamily K member 9 Neighboring gene uncharacterized LOC105375777 Neighboring gene Sharpr-MPRA regulatory region 15097 Neighboring gene uncharacterized LOC107986981 Neighboring gene uncharacterized LOC105375781 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene paternally expressed 13 Neighboring gene uncharacterized LOC105375779 Neighboring gene Sharpr-MPRA regulatory region 993 Neighboring gene uncharacterized LOC105375782 Neighboring gene chromatin accessibility complex subunit 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Mental retardation, autosomal recessive 13
MedGen: C2750791 OMIM: 613192 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Gene-Smoking Interactions Identify Several Novel Blood Pressure Loci in the Framingham Heart Study.
NHGRI GWA Catalog
Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

Pathways from BioSystems

  • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
    Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
  • COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystem (from REACTOME)
    COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystemCOPII components (known as Sec13p, Sec23p, Sec24p, Sec31p, and Sar1p in yeast) traffic cargo from the endoplasmic reticulum to the ER-Golgi intermediate compartment (ERGIC). COPII-coated vesicles wer...
  • ER to Golgi Anterograde Transport, organism-specific biosystem (from REACTOME)
    ER to Golgi Anterograde Transport, organism-specific biosystemSecretory cargo destined to be secreted or to arrive at the plasma membrane (PM) leaves the ER via distinct exit sites. This cargo is destined for the Golgi apparatus for further processing.
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • RAB GEFs exchange GTP for GDP on RABs, organism-specific biosystem (from REACTOME)
    RAB GEFs exchange GTP for GDP on RABs, organism-specific biosystemHuman cells have more than 60 RAB proteins that are key regulators of intracellular membrane trafficking. These small GTPases contribute to trafficking specificity by localizing to the membranes of d...
  • Transport to the Golgi and subsequent modification, organism-specific biosystem (from REACTOME)
    Transport to the Golgi and subsequent modification, organism-specific biosystemAt least two mechanisms of transport of proteins from the ER to the Golgi have been described. One is a general flow requiring no export signals (Wieland et al, 1987; Martinez-Menarguez et al, 1999)....
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC4737, MGC4769, KIAA1882

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
COPII vesicle coating TAS
Traceable Author Statement
more info
 
cerebral cortex development IMP
Inferred from Mutant Phenotype
more info
PubMed 
neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of NF-kappaB transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
TRAPP complex IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
trans-Golgi network IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
trafficking protein particle complex subunit 9
Names
IKK2 binding protein
NIK and IKK-beta binding protein
NIK- and IKBKB-binding protein
TRAPP 120 kDa subunit
tularik gene 1 protein

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_016478.2 RefSeqGene

    Range
    5001..733237
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001160372.4NP_001153844.1  trafficking protein particle complex subunit 9 isoform b

    See identical proteins and their annotated locations for NP_001153844.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The resulting isoform (b) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AB067469, AC007869, AC040978, AC091022, DA228705, DA778234, R49592
    Consensus CDS
    CCDS55278.1
    UniProtKB/Swiss-Prot
    Q96Q05
    Related
    ENSP00000498020.1, ENST00000648948.1
    Conserved Domains (1) summary
    pfam08626
    Location:141100
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit
  2. NM_001321646.2NP_001308575.1  trafficking protein particle complex subunit 9 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' terminal exon and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, and it also lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (c) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AC007869, AC040978, BC006206, DA228705, DA778234, R49592
    UniProtKB/Swiss-Prot
    Q96Q05
    Related
    ENSP00000430116.1, ENST00000520857.5
    Conserved Domains (1) summary
    pfam08626
    Location:141091
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit
  3. NM_031466.7NP_113654.4  trafficking protein particle complex subunit 9 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC007869, AC040978, AC104244, AK128755, R49592
    Consensus CDS
    CCDS34946.1
    UniProtKB/Swiss-Prot
    Q96Q05
    Related
    ENSP00000373979.4, ENST00000389328.8
    Conserved Domains (1) summary
    pfam08626
    Location:1121198
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    139727725..140458579 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017013894.2XP_016869383.1  trafficking protein particle complex subunit 9 isoform X4

  2. XM_011517330.2XP_011515632.1  trafficking protein particle complex subunit 9 isoform X5

    Conserved Domains (1) summary
    pfam08626
    Location:16583
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit
  3. XM_011517326.2XP_011515628.1  trafficking protein particle complex subunit 9 isoform X1

    Conserved Domains (1) summary
    pfam08626
    Location:1121189
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit
  4. XM_011517328.2XP_011515630.1  trafficking protein particle complex subunit 9 isoform X2

    Conserved Domains (1) summary
    pfam08626
    Location:1121094
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit
  5. XM_017013893.1XP_016869382.1  trafficking protein particle complex subunit 9 isoform X3

RNA

  1. XR_928355.2 RNA Sequence

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