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    TRAPPC2L trafficking protein particle complex subunit 2L [ Homo sapiens (human) ]

    Gene ID: 51693, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TRAPPC2Lprovided by HGNC
    Official Full Name
    trafficking protein particle complex subunit 2Lprovided by HGNC
    Primary source
    HGNC:HGNC:30887
    See related
    Ensembl:ENSG00000167515 MIM:610970; AllianceGenome:HGNC:30887
    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
    PERRB; HSPC176
    Summary
    This gene encodes a protein that interacts with the tethering factor trafficking protein particle (TRAPP complex). TRAPP complexes mediate the contact between vescicles and target membranes, and thus, are involved in vescicle-mediated transport of proteins and lipids. The encoded protein is related to the X-linked trafficking protein particle complex 2. A related pseudogene is located on the X chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
    Expression
    Ubiquitous expression in adrenal (RPKM 16.3), testis (RPKM 13.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TRAPPC2L in Genome Data Viewer
    Location:
    16q24.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (88856220..88862678)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (94926614..94933072)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (88922628..88929086)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88869451-88870026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7878 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88870745-88871628 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88871629-88872511 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88873249-88873762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88876670-88877205 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7879 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88878711-88879395 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88879396-88880079 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88882597-88883098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88883099-88883598 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:88884193-88885392 Neighboring gene chromatin licensing and DNA replication factor 1 Neighboring gene adenine phosphoribosyltransferase Neighboring gene galactosamine (N-acetyl)-6-sulfatase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7882 Neighboring gene uncharacterized LOC107983950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7883 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88930168-88930918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11373 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:88940900-88941052 Neighboring gene PABPN1 like, cytoplasmic Neighboring gene uncharacterized LOC101927793 Neighboring gene CBFA2/RUNX1 partner transcriptional co-repressor 3

    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. TRAPPC2L-related disorder: first homozygous protein-truncating variant and further delineation of the phenotype. Abaji M, et al. J Med Genet, 2023 Oct. PMID 36849228
    2. Transcriptional regulation of bidirectional gene pairs by 17-β-estradiol in MCF-7 breast cancer cells. Garcia SA, et al. Braz J Med Biol Res, 2011 Feb. PMID 21180879
    3. A novel homozygous variant in TRAPPC2L results in a neurodevelopmental disorder and disrupts TRAPP complex function. Al-Deri N, et al. J Med Genet, 2021 Sep. PMID 32843486, Free PMC Article
    4. Slow overmethylation of housekeeping genes in the body mucosa is associated with the risk for gastric cancer. Oh JH, et al. Cancer Prev Res (Phila), 2014 Jun. PMID 24654229
    5. Bi-allelic mutations in TRAPPC2L result in a neurodevelopmental disorder and have an impact on RAB11 in fibroblasts. Milev MP, et al. J Med Genet, 2018 Nov. PMID 30120216

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TRAPPC2L-related disorder: first homozygous protein-truncating variant and further delineation of the phenotype.
      Title: TRAPPC2L-related disorder: first homozygous protein-truncating variant and further delineation of the phenotype.
    2. A novel homozygous variant in TRAPPC2L results in a neurodevelopmental disorder and disrupts TRAPP complex function.
      Title: A novel homozygous variant in TRAPPC2L results in a neurodevelopmental disorder and disrupts TRAPP complex function.
    3. deleterious bi-allelic variants in TRAPPC2L are associated with encephalopathy and febrile illness-induced episodes of rhabdomyolysis and subsequent developmental arrest. While the exact pathophysiological route deserves further study, our results suggest a role for RAB11.
      Title: Bi-allelic mutations in TRAPPC2L result in a neurodevelopmental disorder and have an impact on RAB11 in fibroblasts.
    Submit: New GeneRIF Correction

    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

    Associated conditions

    Description Tests
    Encephalopathy, progressive, early-onset, with episodic rhabdomyolysis
    MedGen: C5193033 OMIM: 618331 GeneReviews: Not available
    		not available

    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

    • FLJ44827, MGC111156

    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 COPII vesicle coating NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 TRAPP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of TRAPP complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of TRAPPII protein complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of TRAPPIII protein complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    trafficking protein particle complex subunit 2-like protein
    Names
    hematopoietic stem/progenitor cells 176
    trafficking protein particle complex 2 like

    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_001318524.2 → NP_001305453.1  trafficking protein particle complex subunit 2-like protein isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      BC011369, BC017440, BX419849, DA209193
      Consensus CDS
      CCDS82027.1
      UniProtKB/TrEMBL
      A0A0B4J294
      Related
      ENSP00000457728.1, ENST00000568583.5
      Conserved Domains (1) summary
      pfam04628
      Location:7 → 144
      Sedlin_N; Sedlin, N-terminal conserved region

    2. NM_001318525.2 → NP_001305454.1  trafficking protein particle complex subunit 2-like protein isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 3, which is shorter than isoform 1.
      Source sequence(s)
      BC011369, BC017440, DA209193
      Consensus CDS
      CCDS92207.1
      UniProtKB/Swiss-Prot
      Q9UL33
      Related
      ENSP00000512526.1, ENST00000696289.1
      Conserved Domains (1) summary
      cd14854
      Location:3 → 135
      TRAPPC2L; Trafficking protein particle complex subunit 2-like

    3. NM_001318526.2 → NP_001305455.1  trafficking protein particle complex subunit 2-like protein isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, contains multiple coding region differences and uses an alternate start codon, compared to variant 1. It encodes isoform 4, which is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      BC011369, BC017440, BG283878, BI754306, DA209193, DA833474
      Consensus CDS
      CCDS82029.1
      UniProtKB/TrEMBL
      H3BQQ8
      Related
      ENSP00000455892.1, ENST00000561840.1
      Conserved Domains (1) summary
      cl21566
      Location:54 → 127
      Sedlin_N; Sedlin, N-terminal conserved region

    4. NM_001318527.2 → NP_001305456.1  trafficking protein particle complex subunit 2-like protein isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region and uses an alternate start codon, compared to variant 1. It encodes isoform 5, which is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK307253, AK310805, BC011369, BC017440, BC105809, BX340702, BX419849
      UniProtKB/Swiss-Prot
      Q9UL33
      Conserved Domains (1) summary
      cl21566
      Location:33 → 111
      Sedlin_N; Sedlin, N-terminal conserved region

    5. NM_001318528.2 → NP_001305457.1  trafficking protein particle complex subunit 2-like protein isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream start codon and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 6, which is shorter than isoform 1.
      Source sequence(s)
      AK310805, BC011369, BC017440, DA295904
      UniProtKB/Swiss-Prot
      Q9UL33
      Conserved Domains (1) summary
      pfam04628
      Location:1 → 108
      Sedlin_N; Sedlin, N-terminal conserved region

    6. NM_001318529.2 → NP_001305458.1  trafficking protein particle complex subunit 2-like protein isoform 7

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR and 5' coding region, uses an alternate start codon and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 7, which is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      BC011369, BC017440, BX384775, DA209193
      UniProtKB/Swiss-Prot
      Q9UL33
      Conserved Domains (1) summary
      cl21566
      Location:33 → 105
      Sedlin_N; Sedlin, N-terminal conserved region

    7. NM_001318530.2 → NP_001305459.1  trafficking protein particle complex subunit 2-like protein isoform 8

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream start codon and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 8, which is shorter than isoform 1.
      Source sequence(s)
      BC011369, BC017440, DA833474
      Consensus CDS
      CCDS82028.1
      UniProtKB/TrEMBL
      H3BUK6
      Related
      ENSP00000457684.1, ENST00000567895.5
      Conserved Domains (1) summary
      cd14854
      Location:2 → 105
      TRAPPC2L; Trafficking protein particle complex subunit 2-like

    8. NM_001318532.2 → NP_001305461.1  trafficking protein particle complex subunit 2-like protein isoform 9

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) differs in the 5' UTR and 5' coding region, uses an alternate start codon and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 9, which is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK310805, BC011369, BC017440, DA209193
      UniProtKB/Swiss-Prot
      Q9UL33
      Conserved Domains (1) summary
      cl21566
      Location:33 → 104
      Sedlin_N; Sedlin, N-terminal conserved region

    9. NM_016209.5 → NP_057293.1  trafficking protein particle complex subunit 2-like protein isoform 2

      See identical proteins and their annotated locations for NP_057293.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      BC011369, BC017440, BC105809
      Consensus CDS
      CCDS10971.1
      UniProtKB/Swiss-Prot
      B2R4M9, Q6ZTA7, Q9NZZ4, Q9UL33
      Related
      ENSP00000301021.3, ENST00000301021.7
      Conserved Domains (1) summary
      cd14854
      Location:3 → 136
      TRAPPC2L; Trafficking protein particle complex subunit 2-like

    RNA

    1. NR_134670.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) contains multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC011369, BC017440, BC105809, BI754306

    2. NR_134671.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11) contains multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK307253, AK310805, BC011369, BC017440

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      88856220..88862678
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017023270.1 → XP_016878759.1  trafficking protein particle complex subunit 2-like protein isoform X1

      UniProtKB/TrEMBL
      H3BQQ8
      Conserved Domains (1) summary
      cl21566
      Location:54 → 127
      Sedlin_N; Sedlin, N-terminal conserved region

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      94926614..94933072
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054380442.1 → XP_054236417.1  trafficking protein particle complex subunit 2-like protein isoform X1

      UniProtKB/TrEMBL
      H3BQQ8
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UL33.1 GenPept UniProtKB/Swiss-Prot:Q9UL33

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