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TRAPPC13 trafficking protein particle complex subunit 13 [ Homo sapiens (human) ]

Gene ID: 80006, updated on 2-Nov-2024

Summary

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Official Symbol
TRAPPC13provided by HGNC
Official Full Name
trafficking protein particle complex subunit 13provided by HGNC
Primary source
HGNC:HGNC:25828
See related
Ensembl:ENSG00000113597 AllianceGenome:HGNC:25828
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SHLD3; C5orf44
Summary
Predicted to be located in cytosol. Predicted to be part of TRAPPIII protein complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in prostate (RPKM 7.6), thyroid (RPKM 6.9) and 25 other tissues See more
Orthologs
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Genomic context

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See TRAPPC13 in Genome Data Viewer
Location:
5q12.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (65625027..65666233)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (66446811..66488005)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (64920854..64962060)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:64858912-64859572 Neighboring gene peptidylprolyl isomerase domain and WD repeat containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22608 Neighboring gene RNA, U6 small nuclear 540, pseudogene Neighboring gene tripartite motif containing 23 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:64934876-64935323 Neighboring gene shieldin complex subunit 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22609 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:65015266-65015462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16056 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:65018623-65019444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16058 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16057 Neighboring gene small glutamine rich tetratricopeptide repeat co-chaperone beta Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16059 Neighboring gene PRAME family member 17 pseudogene Neighboring gene neurolysin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16060 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:65220503-65221127 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:65221752-65222376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22612 Neighboring gene LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) pseudogene Neighboring gene erbb2 interacting protein

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. TRAPPC13 modulates autophagy and the response to Golgi stress. Ramírez-Peinado S, et al. J Cell Sci, 2017 Jul 15. PMID 28536105, Free PMC Article
  2. A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Bassik MC, et al. Cell, 2013 Feb 14. PMID 23394947, Free PMC Article
  3. Organization and assembly of the TRAPPII complex. Choi C, et al. Traffic, 2011 Jun. PMID 21453443
  4. PEA15 regulates the DNA damage-induced cell cycle checkpoint and oncogene-directed transformation. Nagarajan A, et al. Mol Cell Biol, 2014 Jun. PMID 24710276, Free PMC Article
  5. TRAPP Complexes in Secretion and Autophagy. Kim JJ, et al. Front Cell Dev Biol, 2016. PMID 27066478, Free PMC Article

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

  • FLJ13611, FLJ26957, MGC48585

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport NAS
Non-traceable Author Statement
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
part_of TRAPPII protein complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of TRAPPIII protein complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm NAS
Non-traceable Author Statement
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
trafficking protein particle complex subunit 13
Names
REV7-interacting novel NHEJ regulator 1
Trs65-related
UPF0533 protein C5orf44
trafficking protein particle complex 13

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_001093755.2 → NP_001087224.1  trafficking protein particle complex subunit 13 isoform 1

    See identical proteins and their annotated locations for NP_001087224.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC008560, AK023673, AL713699, BC012006, BM664695, DB145758, N67829
    Consensus CDS
    CCDS47221.1
    UniProtKB/TrEMBL
    B7ZLB5
    Related
    ENSP00000409231.2, ENST00000438419.6
    Conserved Domains (1) summary
    pfam06159
    Location:65 → 298
    DUF974; Protein of unknown function (DUF974)

  2. NM_001093756.2 → NP_001087225.1  trafficking protein particle complex subunit 13 isoform 3

    See identical proteins and their annotated locations for NP_001087225.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 3).
    Source sequence(s)
    AC008560, AK023673, AL713699, BC117128, BM664695, DB145758, N67829
    Consensus CDS
    CCDS47223.1
    UniProtKB/TrEMBL
    B7ZLB7
    Related
    ENSP00000231526.4, ENST00000231526.8
    Conserved Domains (1) summary
    pfam06159
    Location:65 → 292
    DUF974; Protein of unknown function (DUF974)

  3. NM_001243737.2 → NP_001230666.1  trafficking protein particle complex subunit 13 isoform 4

    See identical proteins and their annotated locations for NP_001230666.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an exon and uses an alternate splice site in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AC008560, BC142994, DB145758
    Consensus CDS
    CCDS58950.1
    UniProtKB/TrEMBL
    B7ZLB5
    Related
    ENSP00000423405.1, ENST00000505553.5
    Conserved Domains (1) summary
    pfam06159
    Location:65 → 292
    DUF974; Protein of unknown function (DUF974)

  4. NM_001365342.1 → NP_001352271.1  trafficking protein particle complex subunit 13 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC008560, DA236226
    Conserved Domains (1) summary
    pfam06159
    Location:1 → 135
    DUF974; Protein of unknown function (DUF974)

  5. NM_001365343.1 → NP_001352272.1  trafficking protein particle complex subunit 13 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC008560, DA236226
    Conserved Domains (1) summary
    pfam06159
    Location:1 → 135
    DUF974; Protein of unknown function (DUF974)

  6. NM_024941.4 → NP_079217.2  trafficking protein particle complex subunit 13 isoform 2

    See identical proteins and their annotated locations for NP_079217.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 2).
    Source sequence(s)
    AC008560, AK023673, AL713699, BC117128, BM664695, DB145758, N67829
    Consensus CDS
    CCDS47222.1
    UniProtKB/Swiss-Prot
    A5PLN9, Q17RZ9, Q49A23, Q4JHG0, Q6MZG4, Q8TCM2, Q9H8I3
    UniProtKB/TrEMBL
    B7ZLB7
    Related
    ENSP00000382367.3, ENST00000399438.8
    Conserved Domains (1) summary
    pfam06159
    Location:65 → 298
    DUF974; Protein of unknown function (DUF974)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    65625027..65666233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    66446811..66488005
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_003545.1: Suppressed sequence

    Description
    NR_003545.1: This RefSeq was removed because it is now thought that this transcript represents a coding variant on another locus, SHLD3.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A5PLN9.2 GenPept UniProtKB/Swiss-Prot:A5PLN9

Gene LinkOut

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