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    SEC23IP SEC23 interacting protein [ Homo sapiens (human) ]

    Gene ID: 11196, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SEC23IPprovided by HGNC
    Official Full Name
    SEC23 interacting proteinprovided by HGNC
    Primary source
    HGNC:HGNC:17018
    See related
    Ensembl:ENSG00000107651 MIM:617852; AllianceGenome:HGNC:17018
    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
    P125; P125A; iPLA1A; MSTP053; iPLA1beta
    Summary
    This gene encodes a member of the phosphatidic acid preferring-phospholipase A1 family. The encoded protein is localized to endoplasmic reticulum exit sites and plays a critical role in ER-Golgi transport as part of the multimeric coat protein II complex. An orthologous gene in frogs is required for normal neural crest cell development, suggesting that this gene may play a role in Waardenburg syndrome neural crest defects. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Feb 2011]
    Expression
    Ubiquitous expression in thyroid (RPKM 7.9), stomach (RPKM 7.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SEC23IP in Genome Data Viewer
    Location:
    10q26.11-q26.12
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (119892730..119944657)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (120790271..120842184)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (121652242..121704169)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene inositol polyphosphate-5-phosphatase F Neighboring gene uncharacterized LOC105378513 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:121575109-121575271 Neighboring gene phosphatase and actin regulator 2 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:121610009-121610508 Neighboring gene minichromosome maintenance complex binding protein Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_10254 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4133 Neighboring gene NANOG hESC enhancer GRCh37_chr10:121648618-121649156 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:121650957-121651468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:121651469-121651979 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:121651980-121652490 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_10320 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_10351 Neighboring gene microRNA 4682 Neighboring gene NACA pseudogene 2

    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. Determination of functional regions of p125, a novel mammalian Sec23p-interacting protein. Mizoguchi T, et al. Biochem Biophys Res Commun, 2000 Dec 9. PMID 11112430
    2. A cascade of ER exit site assembly that is regulated by p125A and lipid signals. Klinkenberg D, et al. J Cell Sci, 2014 Apr 15. PMID 24522181, Free PMC Article
    3. p125A exists as part of the mammalian Sec13/Sec31 COPII subcomplex to facilitate ER-Golgi transport. Ong YS, et al. J Cell Biol, 2010 Aug 9. PMID 20679433, Free PMC Article
    4. Sec23IP recruits VPS13B/COH1 to ER exit site-Golgi interface for tubular ERGIC formation. Du Y, et al. J Cell Biol, 2024 Dec 2. PMID 39352497,
    5. p125 is a novel mammalian Sec23p-interacting protein with structural similarity to phospholipid-modifying proteins. Tani K, et al. J Biol Chem, 1999 Jul 16. PMID 10400679

    See all (98) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Sec23IP recruits VPS13B/COH1 to ER exit site-Golgi interface for tubular ERGIC formation.
      Title: Sec23IP recruits VPS13B/COH1 to ER exit site-Golgi interface for tubular ERGIC formation.
    2. A basic cluster and a hydrophobic interface in the DDHD and SAM domains, respectively, are required for p125A-mediated functional endoplasmic reticulum exit site assembly.
      Title: A cascade of ER exit site assembly that is regulated by p125A and lipid signals.
    3. Xenopus sec23ip is required for normal neural crest cell development, suggesting a role for the human ortholog in Waardenburg syndrome neural crest defects.
      Title: Systematic discovery of nonobvious human disease models through orthologous phenotypes.
    4. The results suggest that p125A is part of the Sec13/Sec31A subcomplex and facilitates ER export in mammalian cells.
      Title: p125A exists as part of the mammalian Sec13/Sec31 COPII subcomplex to facilitate ER-Golgi transport.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
    6. p125 is a mammalian-specific component of ER exit sites and participates in the organization of this compartment
      Title: p125 is localized in endoplasmic reticulum exit sites and involved in their organization.
    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

    EBI GWAS Catalog

    Description
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phospholipase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi organization TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intracellular protein transport TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in COPII-coated ER to Golgi transport vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in COPII-coated ER to Golgi transport vesicle TAS
    Traceable Author Statement
    more info
    		  
    located_in ER to Golgi transport vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum-Golgi intermediate compartment TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    SEC23-interacting protein
    Names
    intracellular phospholipase A1 beta

    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_001411070.1 → NP_001397999.1  SEC23-interacting protein isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC027672
      Consensus CDS
      CCDS91362.1
      UniProtKB/TrEMBL
      A0A994J542
      Related
      ENSP00000516127.1, ENST00000705471.1

    2. NM_007190.4 → NP_009121.1  SEC23-interacting protein isoform 1

      See identical proteins and their annotated locations for NP_009121.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes a functional protein.
      Source sequence(s)
      AB019435, AC027672, AI093198, BC063800
      Consensus CDS
      CCDS7618.1
      UniProtKB/Swiss-Prot
      D3DRD2, Q8IXH5, Q9BUK5, Q9Y6Y8
      UniProtKB/TrEMBL
      B3KM47
      Related
      ENSP00000358071.3, ENST00000369075.8
      Conserved Domains (3) summary
      cd09584
      Location:638 → 702
      SAM_sec23ip; SAM domain of sec23ip
      smart00454
      Location:641 → 701
      SAM; Sterile alpha motif
      pfam02862
      Location:782 → 988
      DDHD; DDHD domain

    RNA

    1. NR_037771.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC027672, AI093198, AK301517, BC063800, DA942854

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      119892730..119944657
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047424537.1 → XP_047280493.1  SEC23-interacting protein isoform X1

      UniProtKB/Swiss-Prot
      D3DRD2, Q8IXH5, Q9BUK5, Q9Y6Y8

    RNA

    1. XR_246061.3 RNA Sequence

    2. XR_007061940.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      120790271..120842184
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054364654.1 → XP_054220629.1  SEC23-interacting protein isoform X1

    RNA

    1. XR_008488159.1 RNA Sequence

    2. XR_008488160.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y6Y8.1 GenPept UniProtKB/Swiss-Prot:Q9Y6Y8

    Gene LinkOut

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