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    SERINC5 serine incorporator 5 [ Homo sapiens (human) ]

    Gene ID: 256987, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SERINC5provided by HGNC
    Official Full Name
    serine incorporator 5provided by HGNC
    Primary source
    HGNC:HGNC:18825
    See related
    Ensembl:ENSG00000164300 MIM:614551; AllianceGenome:HGNC:18825
    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
    TPO1; C5orf12
    Summary
    Predicted to enable L-serine transmembrane transporter activity. Involved in defense response to virus; detection of virus; and innate immune response. Located in several cellular components, including centrosome; cytosol; and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 21.2), colon (RPKM 21.1) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SERINC5 in Genome Data Viewer
    Location:
    5q14.1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (80111225..80256048, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (80595078..80740399, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (79407048..79551867, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene thrombospondin 4 Neighboring gene tRNA methyltransferase subunit 11-2 pseudogene 2 Neighboring gene MPRA-validated peak5305 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:79366012-79367211 Neighboring gene THBS4 antisense RNA 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:79374873-79376072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16133 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:79380002-79380216 Neighboring gene Sharpr-MPRA regulatory region 11102 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16134 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:79441323-79441824 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:79447797-79448296 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:79454739-79455715 Neighboring gene Sharpr-MPRA regulatory region 551 Neighboring gene Sharpr-MPRA regulatory region 2636 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:79481420-79482241 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79483381-79484211 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:79488158-79488728 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:79487586-79488157 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:79489301-79489871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79493799-79494363 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79494364-79494927 Neighboring gene small nucleolar RNA U13 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79541871-79542373 Neighboring gene Sharpr-MPRA regulatory region 10230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:79545029-79545596 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16136 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79552033-79552966 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79552967-79553900 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79553901-79554832 Neighboring gene Sharpr-MPRA regulatory region 10881 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:79568395-79568638 Neighboring gene keratin 18 pseudogene 45 Neighboring gene actin beta pseudogene

    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. Downregulation of SERINC5 expression in buffy coats of HIV-1-infected patients with detectable or undetectable viral load. Hernández-López EG, et al. Mol Biol Rep, 2021 May. PMID 34097204
    2. Super-Resolution Fluorescence Imaging Reveals That Serine Incorporator Protein 5 Inhibits Human Immunodeficiency Virus Fusion by Disrupting Envelope Glycoprotein Clusters. Chen YC, et al. ACS Nano, 2020 Sep 22. PMID 32441921, Free PMC Article
    3. SERINC5 Is an Unconventional HIV Restriction Factor That Is Upregulated during Myeloid Cell Differentiation. Zutz A, et al. J Innate Immun, 2020. PMID 31935717, Free PMC Article
    4. Disruption of Transmembrane Phosphatidylserine Asymmetry by HIV-1 Incorporated SERINC5 Is Not Responsible for Virus Restriction. Raghunath G, et al. Biomolecules, 2024 May 10. PMID 38785977, Free PMC Article
    5. Characterization of Endogenous SERINC5 Protein as Anti-HIV-1 Factor. Passos V, et al. J Virol, 2019 Dec 15. PMID 31597782, Free PMC Article

    See all (54) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Disruption of Transmembrane Phosphatidylserine Asymmetry by HIV-1 Incorporated SERINC5 Is Not Responsible for Virus Restriction.
      Title: Disruption of Transmembrane Phosphatidylserine Asymmetry by HIV-1 Incorporated SERINC5 Is Not Responsible for Virus Restriction.
    2. Beyond Impairment of Virion Infectivity: New Activities of the Anti-HIV Host Cell Factor SERINC5.
      Title: Beyond Impairment of Virion Infectivity: New Activities of the Anti-HIV Host Cell Factor SERINC5.
    3. Relative resistance of patient-derived envelope sequences to SERINC5-mediated restriction of HIV-1 infectivity.
      Title: Relative resistance of patient-derived envelope sequences to SERINC5-mediated restriction of HIV-1 infectivity.
    4. SERINC5 Mediates a Postintegration Block to HIV-1 Gene Expression in Macrophages.
      Title: SERINC5 Mediates a Postintegration Block to HIV-1 Gene Expression in Macrophages.
    5. Restriction of Influenza A Virus by SERINC5.
      Title: Restriction of Influenza A Virus by SERINC5.
    6. AP-2 Adaptor Complex-Dependent Enhancement of HIV-1 Replication by Nef in the Absence of the Nef/AP-2 Targets SERINC5 and CD4.
      Title: AP-2 Adaptor Complex-Dependent Enhancement of HIV-1 Replication by Nef in the Absence of the Nef/AP-2 Targets SERINC5 and CD4.
    7. Nef enhances HIV-1 replication and infectivity independently of SERINC5 in CEM T cells.
      Title: Nef enhances HIV-1 replication and infectivity independently of SERINC5 in CEM T cells.
    8. SERINC5-Mediated Restriction of HIV-1 Infectivity Correlates with Resistance to Cholesterol Extraction but Not with Lipid Order of Viral Membrane.
      Title: SERINC5-Mediated Restriction of HIV-1 Infectivity Correlates with Resistance to Cholesterol Extraction but Not with Lipid Order of Viral Membrane.
    9. HIV-1 Nef interacts with the cyclin K/CDK13 complex to antagonize SERINC5 for optimal viral infectivity.
      Title: HIV-1 Nef interacts with the cyclin K/CDK13 complex to antagonize SERINC5 for optimal viral infectivity.
    10. Downregulation of SERINC5 expression in buffy coats of HIV-1-infected patients with detectable or undetectable viral load.
      Title: Downregulation of SERINC5 expression in buffy coats of HIV-1-infected patients with detectable or undetectable viral load.
    Submit: New GeneRIF Correction See all GeneRIFs (41)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide analyses of borderline personality features.
    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)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    HIV-1 Nef deleted virus is restricted by SERINC5 at an early step in viral replication PubMed
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of SERINC5 PubMed
    HIV-1 Nef deleted virus replication is restricted by both SERINC3 and SERINC5 (combined effect of SERINC3 and SERINC5 noted) PubMed
    HIV-1 Nef deleted virus is restricted by SERINC5; CRISPR-Cas9 knockout of SERINC5 in cells producing HIV-1 Nef deleted virus enhances the infectivity HIV-1 Nef deleted virus of subsequent target cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef HIV-1 Nef antagonizes SERINC5 incorporation into virions PubMed
    nef HIV-1 (SF2) Nef antagonizes SERINC5-mediated antiviral restriction which depends on Nef dileucine, diacidic, and CAW motifs and amino acids 12-39 PubMed
    nef HIV-1 Nef counteracts restriction of HIV-1 replication by SERINC3 and SERINC5 PubMed
    nef HIV-1 Nef relocalizes SERINC5 to Rab7-positive endosomal compartments and prevents SERINC5 incorporation into virions PubMed
    nef HIV-1 Nef downregulates SERINC5 expression on cell surface which, consequently, prevents incorporation of this protein into virions to an extent that correlates with infectivity enhancement PubMed
    nef HIV-1 Nef antagonizes SERINC5-mediated antiviral restriction in CEMT4 T cells PubMed
    nef HIV-1 Nef downregulates cell (CEMT4) surface expression of SERINC5 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

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables L-serine transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in L-serine biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in L-serine transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in defense response to virus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in detection of virus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in innate immune response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in myelination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylserine metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in phospholipid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of serine C-palmitoyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in myelin sheath IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    serine incorporator 5

    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_001174071.3 → NP_001167542.1  serine incorporator 5 isoform 3

      See identical proteins and their annotated locations for NP_001167542.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice pattern in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC010260, AC012636, AF498273, BC101283
      Consensus CDS
      CCDS83009.1
      UniProtKB/TrEMBL
      A0A0J9YYI4
      Related
      ENSP00000426134.2, ENST00000509193.6
      Conserved Domains (1) summary
      pfam03348
      Location:13 → 413
      Serinc; Serine incorporator (Serinc)

    2. NM_001174072.3 → NP_001167543.1  serine incorporator 5 isoform 1

      See identical proteins and their annotated locations for NP_001167543.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC010260, AK297467, BU681476
      Consensus CDS
      CCDS54874.1
      UniProtKB/TrEMBL
      A0A0J9YYI4
      Related
      ENSP00000426237.3, ENST00000507668.7
      Conserved Domains (1) summary
      pfam03348
      Location:13 → 458
      Serinc; Serine incorporator (Serinc)

    3. NM_178276.7 → NP_840060.1  serine incorporator 5 isoform 2

      See identical proteins and their annotated locations for NP_840060.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice pattern in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC010260, AC012636, AF498273
      UniProtKB/Swiss-Prot
      B4DMH7, Q495A4, Q495A6, Q86VE9
      UniProtKB/TrEMBL
      A0A0J9YYI4
      Conserved Domains (1) summary
      pfam03348
      Location:13 → 413
      Serinc; Serine incorporator (Serinc)

    RNA

    1. NR_126060.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the central region and contains alternate 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC010260, AC012636, AF498273, BC101282

    2. NR_126061.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains alternate 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC010260, AC012636, AF498273, BC101281

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      80111225..80256048 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011543304.2 → XP_011541606.1  serine incorporator 5 isoform X1

      Conserved Domains (1) summary
      pfam03348
      Location:13 → 413
      Serinc; Serine incorporator (Serinc)

    2. XM_047417079.1 → XP_047273035.1  serine incorporator 5 isoform X2

    3. XM_047417080.1 → XP_047273036.1  serine incorporator 5 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      80595078..80740399 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352322.1 → XP_054208297.1  serine incorporator 5 isoform X3

    2. XM_054352320.1 → XP_054208295.1  serine incorporator 5 isoform X1

    3. XM_054352321.1 → XP_054208296.1  serine incorporator 5 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86VE9.1 GenPept UniProtKB/Swiss-Prot:Q86VE9

    Gene LinkOut

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

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