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    TMED4 transmembrane p24 trafficking protein 4 [ Homo sapiens (human) ]

    Gene ID: 222068, updated on 28-Oct-2024

    Summary

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    Official Symbol
    TMED4provided by HGNC
    Official Full Name
    transmembrane p24 trafficking protein 4provided by HGNC
    Primary source
    HGNC:HGNC:22301
    See related
    Ensembl:ENSG00000158604 MIM:612038; AllianceGenome:HGNC:22301
    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
    HNLF; ERS25; p24a3; GMP25iso; p24alpha3
    Summary
    Predicted to enable cargo receptor activity. Involved in positive regulation of canonical NF-kappaB signal transduction. Predicted to be located in endoplasmic reticulum membrane. Predicted to be active in several cellular components, including COPII-coated ER to Golgi transport vesicle; Golgi apparatus; and endoplasmic reticulum-Golgi intermediate compartment. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 37.8), small intestine (RPKM 27.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TMED4 in Genome Data Viewer
    Location:
    7p13
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (44577894..44582231, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (44737656..44741987, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (44617493..44621830, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene NPC1 like intracellular cholesterol transporter 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25941 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44579601-44580222 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44600956-44601850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44605263-44605762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25943 Neighboring gene DEAD-box helicase 56 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18147 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44646637-44647200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25948 Neighboring gene oxoglutarate dehydrogenase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25949 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:44674956-44675111 Neighboring gene OGDH intron CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25951 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:44679045-44679572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44685039-44685539 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:44717745-44717958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44740093-44740593 Neighboring gene uncharacterized LOC124901622

    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. Novel oxidative stress-responsive gene ERS25 functions as a regulator of the heat-shock and cell death response. Hwang SO, et al. J Biol Chem, 2008 May 9. PMID 18326488, Free PMC Article
    2. The addition of 5'-coding information to a 3'-directed cDNA library improves analysis of gene expression. Matoba R, et al. Gene, 1994 Sep 2. PMID 8076819
    3. Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes. Tsuritani K, et al. Genome Res, 2007 Jul. PMID 17567985, Free PMC Article
    4. A protein interaction network for Ecm29 links the 26 S proteasome to molecular motors and endosomal components. Gorbea C, et al. J Biol Chem, 2010 Oct 8. PMID 20682791, Free PMC Article
    5. Proteomic analysis reveals novel ligands and substrates for LNX1 E3 ubiquitin ligase. Lenihan JA, et al. PLoS One, 2017. PMID 29121065, Free PMC Article

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ERS25 may play a critical role in regulation of heat-shock response and apoptosis
      Title: Novel oxidative stress-responsive gene ERS25 functions as a regulator of the heat-shock and cell death response.
    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

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev is identified to have a physical interaction with transmembrane emp24 protein transport domain containing 4 (TMED4) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: DDX56

    Homology

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in Golgi organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of canonical NF-kappaB signal transduction HMP PubMed 
    Component Evidence Code Pubs
    is_active_in COPII-coated ER to Golgi transport vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endoplasmic reticulum-Golgi intermediate compartment IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    transmembrane emp24 domain-containing protein 4
    Names
    endoplasmic reticulum stress-response protein 25 kDa
    p24 family protein alpha-3
    putative NF-kappa-B-activating protein 156
    putative NFkB activating protein HNLF
    transmembrane emp24 protein transport domain containing 4

    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_001303058.2 → NP_001289987.1  transmembrane emp24 domain-containing protein 4 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001289987.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK074557, BM857430
      Consensus CDS
      CCDS78227.1
      UniProtKB/Swiss-Prot
      Q7Z7H5
      Related
      ENSP00000417443.1, ENST00000481238.1
      Conserved Domains (1) summary
      pfam01105
      Location:29 → 179
      EMP24_GP25L; emp24/gp25L/p24 family/GOLD

    2. NM_001303059.2 → NP_001289988.1  transmembrane emp24 domain-containing protein 4 isoform 3 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AC004938, BC035467, BP872004, BX647965, DA419871
      Consensus CDS
      CCDS78226.1
      UniProtKB/TrEMBL
      F8W7F7
      Related
      ENSP00000289577.5, ENST00000289577.10
      Conserved Domains (1) summary
      pfam01105
      Location:29 → 173
      EMP24_GP25L; emp24/gp25L/p24 family/GOLD

    3. NM_001303060.2 → NP_001289989.1  transmembrane emp24 domain-containing protein 4 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains multiple differences in the both the 5' and 3' exon structure, compared to variant 1, and initiates translation at a downstream start codon. The encoded isoform (4) has a shorter N-terminus and distinct C-terminus, and is shorter than isoform 1.
      Source sequence(s)
      AK074557, BC025705, BM857430, DA419871
      UniProtKB/Swiss-Prot
      Q7Z7H5
      Related
      ENST00000477639.5
      Conserved Domains (1) summary
      pfam01105
      Location:7 → 120
      EMP24_GP25L; emp24/gp25L/p24 family/GOLD

    4. NM_001303061.2 → NP_001289990.1  transmembrane emp24 domain-containing protein 4 isoform 5

      See identical proteins and their annotated locations for NP_001289990.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in the 5' region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (5) has a shorter N-terminus than isoform 1. Variants 5 and 6 encode the same isoform (5).
      Source sequence(s)
      AC004938, AL602839, BC035467, BX647965, DA419871
      Conserved Domains (1) summary
      pfam01105
      Location:15 → 163
      EMP24_GP25L; emp24/gp25L/p24 family/GOLD

    5. NM_001303062.2 → NP_001289991.1  transmembrane emp24 domain-containing protein 4 isoform 5

      See identical proteins and their annotated locations for NP_001289991.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) contains an alternate segment in the 5' region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (5) has a shorter N-terminus than isoform 1. Variants 5 and 6 encode the same isoform (5).
      Source sequence(s)
      AC004938, BC025705, BC035467, BX461603, BX647965, DA419871
      Conserved Domains (1) summary
      pfam01105
      Location:15 → 163
      EMP24_GP25L; emp24/gp25L/p24 family/GOLD

    6. NM_182547.4 → NP_872353.2  transmembrane emp24 domain-containing protein 4 isoform 1 precursor

      See identical proteins and their annotated locations for NP_872353.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC004938, BC035467, BC052641, BX647965, DA419871
      Consensus CDS
      CCDS5493.1
      UniProtKB/Swiss-Prot
      A4D2K8, B4DFJ4, Q56VW3, Q7Z432, Q7Z7H5, Q8N2P6
      Related
      ENSP00000404042.2, ENST00000457408.7
      Conserved Domains (1) summary
      pfam01105
      Location:29 → 222
      EMP24_GP25L; emp24/gp25L/p24 family/GOLD

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      44577894..44582231 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      44737656..44741987 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z7H5.1 GenPept UniProtKB/Swiss-Prot:Q7Z7H5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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