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SERINC5 serine incorporator 5 [ Homo sapiens (human) ]

Gene ID: 256987, updated on 28-Oct-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, Oct 2024]
Expression
Broad expression in testis (RPKM 21.2), colon (RPKM 21.1) and 24 other tissues See more
Orthologs
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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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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
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

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