PLSCR1 phospholipid scramblase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PLSCR1provided by HGNC
Official Full Name: phospholipid scramblase 1provided by HGNC
Primary source: HGNC:HGNC:9092
See related: Ensembl:ENSG00000188313 MIM:604170; AllianceGenome:HGNC:9092
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: MMTRA1B
Summary: This gene encodes a phospholipid scramblase family member. The encoded protein is involved in disruption of the asymmetrical distribution of phospholipids between the inner and outer leaflets of the plasma membrane, resulting in externalization of phosphatidylserine. This cell membrane disruption plays an important role in the blood coagulation cascade as well as macrophage clearing of apoptotic cells. The encoded protein has additionally been implicated in gene regulation and interferon-induced antiviral responses. [provided by RefSeq, May 2022]
Annotation information: Note: This gene has been reviewed for its involvement in coronavirus biology, and is involved in immune response or antiviral activity.
Expression: Ubiquitous expression in appendix (RPKM 43.5), gall bladder (RPKM 33.7) and 25 other tissues See more
Orthologs: all
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Genomic context

Location:: 3q24

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (146515180..146544607, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (149270345..149299772, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (146232967..146262394, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

PLSCR1 is a cell-autonomous defence factor against SARS-CoV-2 infection.
Title: PLSCR1 is a cell-autonomous defence factor against SARS-CoV-2 infection.
Biophysical characterization of the DNA binding motif of human phospholipid scramblase 1.
Title: Biophysical characterization of the DNA binding motif of human phospholipid scramblase 1.
Interaction of human phospholipid scramblase 1 with cholesterol via CRAC motif is essential for functional regulation and subcellular localization.
Title: Interaction of human phospholipid scramblase 1 with cholesterol via CRAC motif is essential for functional regulation and subcellular localization.
The Interferon-Inducible Human PLSCR1 Protein Is a Restriction Factor of Human Cytomegalovirus.
Title: The Interferon-Inducible Human PLSCR1 Protein Is a Restriction Factor of Human Cytomegalovirus.
The ratio of ATP11C/PLSCR1 mRNA transcripts has clinical significance in sickle cell anemia.
Title: The ratio of ATP11C/PLSCR1 mRNA transcripts has clinical significance in sickle cell anemia.
Nuclear accumulation of KPNA2 impacts radioresistance through positive regulation of the PLSCR1-STAT1 loop in lung adenocarcinoma.
Title: Nuclear accumulation of KPNA2 impacts radioresistance through positive regulation of the PLSCR1-STAT1 loop in lung adenocarcinoma.
MicroRNA-628-5p inhibits invasion and migration of human pancreatic ductal adenocarcinoma via suppression of the AKT/NF-kappa B pathway.
Title: MicroRNA-628-5p inhibits invasion and migration of human pancreatic ductal adenocarcinoma via suppression of the AKT/NF-kappa B pathway.
Nuclear translocation of PLSCR1 activates STAT1 signaling in basal-like breast cancer.
Title: Nuclear translocation of PLSCR1 activates STAT1 signaling in basal-like breast cancer.
Transient Receptor Potential Canonical 5-Scramblase Signaling Complex Mediates Neuronal Phosphatidylserine Externalization and Apoptosis.
Title: Transient Receptor Potential Canonical 5-Scramblase Signaling Complex Mediates Neuronal Phosphatidylserine Externalization and Apoptosis.
Heterogeneous ozone effects on the DNA methylome of bronchial cells observed in a crossover study.
Title: Heterogeneous ozone effects on the DNA methylome of bronchial cells observed in a crossover study.

Submit: New GeneRIF Correction See all GeneRIFs (66)

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

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
Knockdown of phospholipid scramblase 1 (PLSCR1) by shRNA enhances the levels of gag mRNA in an HIV-1-infected MOLT-4 cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	Overexpression of PLSCR1 inhibits HIV-1 Tat-mediated transactivation of the HIV-1 LTR and reduces the nuclear translocation of Tat	PubMed
	tat	Human phospholipid scramblase 1 (PLSCR1) directly interacts with HIV-1 Tat both in vitro and in vivo through amino acids 160-250 of PLSCR1	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

PMC229255P5 (e-PCR)
- UniSTS:272172

SHGC-77431 (e-PCR)
- UniSTS:48456

SHGC-77437 (e-PCR)
- UniSTS:51388

SGC32718 (e-PCR)
- UniSTS:45767

STS-N33501 (e-PCR)
- UniSTS:20445

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables CD4 receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables SH3 domain binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	NAS Non-traceable Author Statement more info	PubMed
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables epidermal growth factor receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables lead ion binding	IDA Inferred from Direct Assay more info	PubMed
enables magnesium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables mercury ion binding	IDA Inferred from Direct Assay more info	PubMed
enables nuclease activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables phospholipid scramblase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phospholipid scramblase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables virus receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in acute-phase response	ISS Inferred from Sequence or Structural Similarity more info
involved_in apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in defense response to virus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of phagocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of viral genome replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in phosphatidylserine biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in phosphatidylserine exposure on apoptotic cell surface	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in plasma membrane phospholipid scrambling	IBA Inferred from Biological aspect of Ancestor more info
involved_in plasma membrane phospholipid scrambling	IDA Inferred from Direct Assay more info	PubMed
involved_in platelet activation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of chromosome separation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of innate immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of Fc receptor mediated stimulatory signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of mast cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to interferon-beta	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to lead ion	IDA Inferred from Direct Assay more info	PubMed
involved_in symbiont entry into host cell	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in collagen-containing extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in membrane	HDA more info	PubMed
located_in membrane raft	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: phospholipid scramblase 1

Names: PL scramblase 1; ca(2+)-dependent phospholipid scramblase 1; erythrocyte phospholipid scramblase; mg(2+)-dependent nuclease

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_001363872.1 → NP_001350801.1 phospholipid scramblase 1 isoform 2

Status: REVIEWED

Source sequence(s)

AC069528, AC116544

Consensus CDS

CCDS87153.1

UniProtKB/TrEMBL

C9J7K9

Related

ENSP00000417792.1, ENST00000487389.5

Conserved Domains (2) summary

pfam03803
Location:79 → 300

Scramblase; Scramblase

cl27975
Location:15 → 90

EBV-NA3; Epstein-Barr virus nuclear antigen 3 (EBNA-3)
NM_001363874.1 → NP_001350803.1 phospholipid scramblase 1 isoform 3

Status: REVIEWED

Source sequence(s)

AC069528, AC116544

Consensus CDS

CCDS87152.1

Conserved Domains (1) summary

pfam03803
Location:22 → 226

Scramblase; Scramblase
NM_001406033.1 → NP_001392962.1 phospholipid scramblase 1 isoform 4

Status: REVIEWED

Source sequence(s)

AC069528, AC116544
NM_001406034.1 → NP_001392963.1 phospholipid scramblase 1 isoform 1

Status: REVIEWED

Source sequence(s)

AC069528, AC116544

Consensus CDS

CCDS3135.1

UniProtKB/Swiss-Prot

B2R8H8, B4DTE8, O15162
NM_001406035.1 → NP_001392964.1 phospholipid scramblase 1 isoform 1

Status: REVIEWED

Source sequence(s)

AC069528, AC116544

Consensus CDS

CCDS3135.1

UniProtKB/Swiss-Prot

B2R8H8, B4DTE8, O15162
NM_001406036.1 → NP_001392965.1 phospholipid scramblase 1 isoform 5

Status: REVIEWED

Source sequence(s)

AC069528, AC116544

Related

ENSP00000418103.1, ENST00000462666.5
NM_001406037.1 → NP_001392966.1 phospholipid scramblase 1 isoform 6

Status: REVIEWED

Source sequence(s)

AC069528, AC116544
NM_001406038.1 → NP_001392967.1 phospholipid scramblase 1 isoform 3

Status: REVIEWED

Source sequence(s)

AC069528, AC116544

Consensus CDS

CCDS87152.1
NM_001406039.1 → NP_001392968.1 phospholipid scramblase 1 isoform 3

Status: REVIEWED

Source sequence(s)

AC069528, AC116544
NM_001406040.1 → NP_001392969.1 phospholipid scramblase 1 isoform 3

Status: REVIEWED

Source sequence(s)

AC069528, AC116544
NM_001406041.1 → NP_001392970.1 phospholipid scramblase 1 isoform 3

Status: REVIEWED

Source sequence(s)

AC069528, AC116544

Related

ENSP00000411675.2, ENST00000448787.6
NM_001406042.1 → NP_001392971.1 phospholipid scramblase 1 isoform 7

Status: REVIEWED

Source sequence(s)

AC069528, AC116544
NM_021105.3 → NP_066928.1 phospholipid scramblase 1 isoform 1

See identical proteins and their annotated locations for NP_066928.1

Status: REVIEWED

Source sequence(s)

AF098642, BC032718

Consensus CDS

CCDS3135.1

UniProtKB/Swiss-Prot

B2R8H8, B4DTE8, O15162

Related

ENSP00000345494.4, ENST00000342435.9

Conserved Domains (2) summary

pfam03803
Location:86 → 307

Scramblase; Scramblase

cl23807
Location:20 → 100

WWbp; WW-domain ligand protein

RNA

NR_175994.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC069528, AC116544
NR_175995.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC069528, AC116544
NR_175996.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC069528, AC116544

Related

ENST00000493432.5
NR_175997.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC069528, AC116544
NR_175998.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC069528, AC116544
NR_175999.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC069528, AC116544
NR_176000.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC069528, AC116544
NR_176001.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC069528, AC116544
NR_176002.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC069528, AC116544