SERINC5 serine incorporator 5 [Homo sapiens (human)] - Gene

Summary

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, Apr 2022]
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

Location:: 5q14.1

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (80111225..80256048, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (80595078..80740399, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (79407048..79551867, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
Restriction of Influenza A Virus by SERINC5.
Title: Restriction of Influenza A Virus by SERINC5.
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.
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.
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.
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.
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.
HIV envelope tail truncation confers resistance to SERINC5 restriction.
Title: HIV envelope tail truncation confers resistance to SERINC5 restriction.

Submit: New GeneRIF Correction See all GeneRIFs (40)

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

D10S275 (e-PCR)
- UniSTS:147992

SHGC-35055 (e-PCR)
- UniSTS:65572

D5S2675 (e-PCR)
- UniSTS:73256

RH68715 (e-PCR)
- UniSTS:25649

L28256 (e-PCR)
- UniSTS:32152

RH16321 (e-PCR)
- UniSTS:28081

RH68505 (e-PCR)
- UniSTS:7609

D5S2485 (e-PCR)
- UniSTS:43716

STS-T96036 (e-PCR)
- UniSTS:57284

SHGC-33799 (e-PCR)
- UniSTS:57285

A006W30 (e-PCR)
- UniSTS:43211

RH78501 (e-PCR)
- UniSTS:41677

NIB1185 (e-PCR)
- UniSTS:41678

NoName (e-PCR)
- UniSTS:484578

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 more info	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)

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, ENST00000509193.5

Conserved Domains (1) summary

pfam03348
Location:13 → 413

Serinc; Serine incorporator (Serinc)
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)
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

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
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

80111225..80256048 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (1) summary

pfam03348
Location:13 → 413

Serinc; Serine incorporator (Serinc)
XM_047417079.1 → XP_047273035.1 serine incorporator 5 isoform X2
XM_047417080.1 → XP_047273036.1 serine incorporator 5 isoform X3