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

Gene ID: 76510, updated on 12-May-2024

Summary

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 non-syndromic intellectual disability. Orthologous to human TRAPPC9 (trafficking protein particle complex subunit 9). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in adrenal adult (RPKM 14.2), genital fat pad adult (RPKM 11.4) and 28 other tissues See more
Orthologs
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Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • KIAA1882

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
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

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_001164641.1NP_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:70795
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit
  2. NM_001164643.1NP_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:70494
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit
  3. NM_029640.2NP_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:10914
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit
  4. NM_180662.2NP_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:701093
    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_006521527.5XP_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:701102
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit
  2. XM_017316788.2XP_017172277.1  trafficking protein particle complex subunit 9 isoform X2

    Conserved Domains (1) summary
    pfam08626
    Location:10905
    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.