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

Gene ID: 222068, updated on 5-Mar-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
Involved in positive regulation of I-kappaB kinase/NF-kappaB signaling. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of 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, Apr 2022]
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_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (44577894..44582231, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (44737656..44741987, complement)
105.20220307 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
  • 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 (43) 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

Function Evidence Code Pubs
enables cargo receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
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, ENST00000289577.9
    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_2023_10

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

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