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SEC24D SEC24 homolog D, COPII coat complex component [ Homo sapiens (human) ]

Gene ID: 9871, updated on 7-Dec-2018

Summary

Official Symbol
SEC24Dprovided by HGNC
Official Full Name
SEC24 homolog D, COPII coat complex componentprovided by HGNC
Primary source
HGNC:HGNC:10706
See related
Ensembl:ENSG00000150961 MIM:607186
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
CLCRP2
Summary
The protein encoded by this gene is a member of the SEC24 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein has similarity to yeast Sec24p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. This gene product is implicated in the shaping of the vesicle, and also in cargo selection and concentration. Mutations in this gene have been associated with Cole-Carpenter syndrome, a disorder affecting bone formation, resulting in craniofacial malformations and bones that break easily. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
Expression
Ubiquitous expression in thyroid (RPKM 21.6), small intestine (RPKM 18.5) and 25 other tissues See more
Orthologs

Genomic context

See SEC24D in Genome Data Viewer
Location:
4q26
Exon count:
25
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (118722823..118838683, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (119643978..119759838, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene METTL14 divergent transcript Neighboring gene methyltransferase like 14 Neighboring gene uncharacterized LOC105377393 Neighboring gene synaptopodin 2 Neighboring gene uncharacterized LOC105377394

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Antigen Presentation: Folding, assembly and peptide loading of class I MHC, organism-specific biosystem (from REACTOME)
    Antigen Presentation: Folding, assembly and peptide loading of class I MHC, organism-specific biosystemUnlike other glycoproteins, correct folding of MHC class I molecules is not sufficient to trigger their exit from the ER, they exit only after peptide loading. Described here is the process of antige...
  • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
    Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
  • COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystem (from REACTOME)
    COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystemCOPII components (known as Sec13p, Sec23p, Sec24p, Sec31p, and Sar1p in yeast) traffic cargo from the endoplasmic reticulum to the ER-Golgi intermediate compartment (ERGIC). COPII-coated vesicles wer...
  • COPII complex, organism-specific biosystem (from KEGG)
    COPII complex, organism-specific biosystemStructural complex; Genetic information processing; Protein processing
  • COPII complex, conserved biosystem (from KEGG)
    COPII complex, conserved biosystemStructural complex; Genetic information processing; Protein processing
  • Cargo concentration in the ER, organism-specific biosystem (from REACTOME)
    Cargo concentration in the ER, organism-specific biosystemComputational analysis suggests that ~25% of the proteome may be exported from the ER in human cells (Kanapin et al, 2003). These cargo need to be recognized and concentrated into COPII vesicles, wh...
  • Class I MHC mediated antigen processing & presentation, organism-specific biosystem (from REACTOME)
    Class I MHC mediated antigen processing & presentation, organism-specific biosystemMajor histocompatibility complex (MHC) class I molecules play an important role in cell mediated immunity by reporting on intracellular events such as viral infection, the presence of intracellular b...
  • ER to Golgi Anterograde Transport, organism-specific biosystem (from REACTOME)
    ER to Golgi Anterograde Transport, organism-specific biosystemSecretory cargo destined to be secreted or to arrive at the plasma membrane (PM) leaves the ER via distinct exit sites. This cargo is destined for the Golgi apparatus for further processing.
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • MHC class II antigen presentation, organism-specific biosystem (from REACTOME)
    MHC class II antigen presentation, organism-specific biosystemAntigen presenting cells (APCs) such as B cells, dendritic cells (DCs) and monocytes/macrophages express major histocompatibility complex class II molecules (MHC II) at their surface and present exog...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Protein processing in endoplasmic reticulum, organism-specific biosystem (from KEGG)
    Protein processing in endoplasmic reticulum, organism-specific biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...
  • Protein processing in endoplasmic reticulum, conserved biosystem (from KEGG)
    Protein processing in endoplasmic reticulum, conserved biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...
  • Regulation of cholesterol biosynthesis by SREBP (SREBF), organism-specific biosystem (from REACTOME)
    Regulation of cholesterol biosynthesis by SREBP (SREBF), organism-specific biosystemSterol regulatory element binding proteins (SREBPs, SREBFs) respond to low cholesterol concentrations by transiting to the nucleus and activating genes involved in cholesterol and lipid biosynthesis ...
  • Sterol Regulatory Element-Binding Proteins (SREBP) signalling, organism-specific biosystem (from WikiPathways)
    Sterol Regulatory Element-Binding Proteins (SREBP) signalling, organism-specific biosystemSterol regulatory element-binding proteins (SREBPs) are membrane-bound proteins that act as transcription factors. They regulate lipid, especially cholesterol, biosynthesis and uptake at a transcript...
  • Transport to the Golgi and subsequent modification, organism-specific biosystem (from REACTOME)
    Transport to the Golgi and subsequent modification, organism-specific biosystemAt least two mechanisms of transport of proteins from the ER to the Golgi have been described. One is a general flow requiring no export signals (Wieland et al, 1987; Martinez-Menarguez et al, 1999)....
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ43974, KIAA0755

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SNARE binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
COPII vesicle coat IDA
Inferred from Direct Assay
more info
PubMed 
COPII vesicle coat NAS
Non-traceable Author Statement
more info
PubMed 
ER to Golgi transport vesicle membrane TAS
Traceable Author Statement
more info
 
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
cytosol TAS
Traceable Author Statement
more info
 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
protein transport protein Sec24D
Names
SEC24 related gene family, member D
SEC24-related protein D

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_042032.1 RefSeqGene

    Range
    4976..118349
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001318066.1NP_001304995.1  protein transport protein Sec24D isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) has the same N- and C-termini, but is one amino acid longer than isoform 1.
    Source sequence(s)
    AF130464, BC035761, DA034453
    UniProtKB/Swiss-Prot
    O94855
    Conserved Domains (2) summary
    cl26464
    Location:8294
    Atrophin-1; Atrophin-1 family
    cl27110
    Location:1821028
    zf-Sec23_Sec24; Sec23/Sec24 zinc finger
  2. NM_014822.4NP_055637.2  protein transport protein Sec24D isoform 1

    See identical proteins and their annotated locations for NP_055637.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).
    Source sequence(s)
    AB018298, AK291765, BC035761, DB224337
    Consensus CDS
    CCDS3710.1
    UniProtKB/Swiss-Prot
    O94855
    UniProtKB/TrEMBL
    A8K6V0
    Related
    ENSP00000280551.6, ENST00000280551.10
    Conserved Domains (2) summary
    pfam09606
    Location:1256
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cl27110
    Location:1321027
    zf-Sec23_Sec24; Sec23/Sec24 zinc finger

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    118722823..118838683 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024454293.1XP_024310061.1  protein transport protein Sec24D isoform X2

    Conserved Domains (2) summary
    pfam09606
    Location:1256
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cl27110
    Location:1321027
    zf-Sec23_Sec24; Sec23/Sec24 zinc finger
  2. XM_005263379.3XP_005263436.1  protein transport protein Sec24D isoform X1

    See identical proteins and their annotated locations for XP_005263436.1

    UniProtKB/Swiss-Prot
    O94855
    Conserved Domains (2) summary
    cl26464
    Location:8294
    Atrophin-1; Atrophin-1 family
    cl27110
    Location:1821028
    zf-Sec23_Sec24; Sec23/Sec24 zinc finger
  3. XM_017008875.1XP_016864364.1  protein transport protein Sec24D isoform X3

    Related
    ENSP00000425491.1, ENST00000511481.5
    Conserved Domains (4) summary
    cd01479
    Location:1252
    Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...
    pfam00626
    Location:455530
    Gelsolin; Gelsolin repeat
    pfam04815
    Location:341437
    Sec23_helical; Sec23/Sec24 helical domain
    pfam08033
    Location:242326
    Sec23_BS; Sec23/Sec24 beta-sandwich domain
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