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PLSCR4 phospholipid scramblase 4 [ Homo sapiens (human) ]

Gene ID: 57088, updated on 7-Apr-2024

Summary

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Official Symbol
PLSCR4provided by HGNC
Official Full Name
phospholipid scramblase 4provided by HGNC
Primary source
HGNC:HGNC:16497
See related
Ensembl:ENSG00000114698 MIM:607612; AllianceGenome:HGNC:16497
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
TRA1
Summary
Enables CD4 receptor binding activity and enzyme binding activity. Predicted to be involved in plasma membrane phospholipid scrambling. Predicted to act upstream of or within cellular response to lipopolysaccharide. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in fat (RPKM 22.0), gall bladder (RPKM 21.1) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
3q24
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (146192335..146251105, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (148947862..149006253, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (145910122..145968892, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:145815129-145815678 Neighboring gene MPRA-validated peak4856 silencer Neighboring gene procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:145852057-145852829 Neighboring gene uncharacterized LOC105374145 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:145974007-145974996 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:145974997-145975985 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:146064530-146065284 Neighboring gene PLSCR4 pseudogene 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:146105286-146106485 Neighboring gene phospholipid scramblase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20672

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. Whole blood transcriptomic analysis reveals PLSCR4 as a potential marker for vaso-occlusive crises in sickle cell disease. Abdulwahab H, et al. Sci Rep, 2021 Nov 12. PMID 34772994, Free PMC Article
  2. Biochemical and functional characterization of human phospholipid scramblase 4 (hPLSCR4). Francis VG, et al. Biol Chem, 2012 Oct. PMID 23089641
  3. Phospholipid Scramblase 4 (PLSCR4) Regulates Adipocyte Differentiation via PIP3-Mediated AKT Activation. Barth LAG, et al. Int J Mol Sci, 2022 Aug 29. PMID 36077184, Free PMC Article
  4. Snail represses the expression of human phospholipid scramblase 4 gene. Vinnakota JM, et al. Gene, 2016 Oct 15. PMID 27363667
  5. A minimal nuclear localization signal (NLS) in human phospholipid scramblase 4 that binds only the minor NLS-binding site of importin alpha1. Lott K, et al. J Biol Chem, 2011 Aug 12. PMID 21690087, Free PMC Article

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Phospholipid Scramblase 4 (PLSCR4) Regulates Adipocyte Differentiation via PIP3-Mediated AKT Activation.
    Title: Phospholipid Scramblase 4 (PLSCR4) Regulates Adipocyte Differentiation via PIP3-Mediated AKT Activation.
  2. Whole blood transcriptomic analysis reveals PLSCR4 as a potential marker for vaso-occlusive crises in sickle cell disease.
    Title: Whole blood transcriptomic analysis reveals PLSCR4 as a potential marker for vaso-occlusive crises in sickle cell disease.
  3. LINC00641 induces the malignant progression of colorectal carcinoma through the miRNA-424-5p/PLSCR4 feedback loop.
    Title: LINC00641 induces the malignant progression of colorectal carcinoma through the miRNA-424-5p/PLSCR4 feedback loop.
  4. Specific DNA methylation signatures for aggressive choroid plexus carcinoma (CPC) revealed AK1, PER2, and PLSCR4 as potential biomarkers for CPC that can be used to improve molecular stratification for diagnosis and treatment.
    Title: DNA methylation signature is prognostic of choroid plexus tumor aggressiveness.
  5. LINC00641 suppressed cell proliferation and induced cell apoptosis in NSCLC, indicating that LINC00641 exerted tumor-suppressive role in NSCLC. Through mechanism investigation, we determined that LINC00641 acted as a competing endogenous RNA (ceRNA) in NSCLC by sponging miR-424-5p to upregulate phospholipid scramblase (PLSCR4) expression.
    Title: Long non-coding RNA LINC00641 suppresses non-small-cell lung cancer by sponging miR-424-5p to upregulate PLSCR4.
  6. the first report on the transcriptional regulation of hPLSCR4, where Snail was shown to downregulate the expression of Human phospholipid scramblase 4
    Title: Snail represses the expression of human phospholipid scramblase 4 gene.
  7. biochemical and functional characterization of human phospholipid scramblase 4
    Title: Biochemical and functional characterization of human phospholipid scramblase 4 (hPLSCR4).
  8. Crystallographic analysis of mammalian importin alpha1 in complex with the hPLSCR4-NLS reveals this minimal NLS binds specifically and exclusively to the minor binding site of importin alpha
    Title: A minimal nuclear localization signal (NLS) in human phospholipid scramblase 4 that binds only the minor NLS-binding site of importin alpha1.
  9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  10. Results show that binding affinities of the peptides are in the order hPLSCR1>hPLSCR3>hPLSCR2>hPLSCR4 for Ca2+ and in the order hPLSCR1>hPLSCR2>hPLSCR3>hPLSCR4 for Mg2+.
    Title: Calcium binding studies of peptides of human phospholipid scramblases 1 to 4 suggest that scramblases are new class of calcium binding proteins in the cell.
Submit: New GeneRIF Correction See all GeneRIFs (11)

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)

Genotypes

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 CD4 receptor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables SH3 domain binding IEA
Inferred from Electronic Annotation
more info
  
enables calcium ion binding NAS
Non-traceable Author Statement
more info
 PubMed 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables phospholipid scramblase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phospholipid scramblase activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
  
involved_in plasma membrane phospholipid scrambling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in plasma membrane phospholipid scrambling NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
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 4
Names
Ca(2+)-dependent phospholipid scramblase 4
PL scramblase 4
cell growth inhibiting protein 43

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_001128304.2 → NP_001121776.1  phospholipid scramblase 4 isoform a

    See identical proteins and their annotated locations for NP_001121776.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1, 2, and 3 all encode isoform a.
    Source sequence(s)
    AC092982, AF199023, AK128442, AW086426, BC028354, DA185957
    UniProtKB/Swiss-Prot
    A8K2E9, Q2TTR3, Q658L3, Q6ZR73, Q7Z505, Q9NRQ2
    UniProtKB/TrEMBL
    B2R720
    Related
    ENSP00000419040.1, ENST00000493382.5
    Conserved Domains (2) summary
    pfam03803
    Location:100 → 322
    Scramblase; Scramblase
    cl26464
    Location:36 → 100
    Atrophin-1; Atrophin-1 family

  2. NM_001128305.2 → NP_001121777.1  phospholipid scramblase 4 isoform a

    See identical proteins and their annotated locations for NP_001121777.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 all encode isoform a.
    Source sequence(s)
    AC092982, AF199023, AK128442, AW086426, BC028354, BP201782
    UniProtKB/Swiss-Prot
    A8K2E9, Q2TTR3, Q658L3, Q6ZR73, Q7Z505, Q9NRQ2
    UniProtKB/TrEMBL
    B2R720
    Related
    ENSP00000399315.2, ENST00000446574.6
    Conserved Domains (2) summary
    pfam03803
    Location:100 → 322
    Scramblase; Scramblase
    cl26464
    Location:36 → 100
    Atrophin-1; Atrophin-1 family

  3. NM_001128306.2 → NP_001121778.1  phospholipid scramblase 4 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks two alternate exons resulting in the loss of an in-frame segment in the central coding region, compared to variant 1. The encoded isoform (b) has the same N- and C-termini but is shorter than isoform a.
    Source sequence(s)
    AC092982, AF199023, AK128442, AW086426, BC028354, DA444235
    UniProtKB/TrEMBL
    E9PHR9
    Related
    ENSP00000372561.2, ENST00000383083.6
    Conserved Domains (2) summary
    cl02043
    Location:103 → 232
    LOR; LURP-one-related
    cl26464
    Location:36 → 152
    Atrophin-1; Atrophin-1 family

  4. NM_001177304.2 → NP_001170775.1  phospholipid scramblase 4 isoform c

    See identical proteins and their annotated locations for NP_001170775.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream start codon, and lacks two alternate exons resulting in the loss of an in-frame segment in the central coding region, compared to variant 1. The resulting isoform (c) is shorter than isoform a.
    Source sequence(s)
    AK128442, AW665992, BC028354, BG538024, BU160106, BU567842
    Consensus CDS
    CCDS54651.1
    UniProtKB/Swiss-Prot
    Q9NRQ2
    Related
    ENSP00000415605.2, ENST00000433593.6
    Conserved Domains (1) summary
    cl02043
    Location:88 → 217
    LOR; LURP-one-related

  5. NM_020353.3 → NP_065086.2  phospholipid scramblase 4 isoform a

    See identical proteins and their annotated locations for NP_065086.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 all encode isoform a.
    Source sequence(s)
    AC092982, AF199023, AK128442, AW086426, BC028354
    Consensus CDS
    CCDS3133.1
    UniProtKB/Swiss-Prot
    A8K2E9, Q2TTR3, Q658L3, Q6ZR73, Q7Z505, Q9NRQ2
    UniProtKB/TrEMBL
    B2R720
    Related
    ENSP00000347038.2, ENST00000354952.7
    Conserved Domains (2) summary
    pfam03803
    Location:100 → 322
    Scramblase; Scramblase
    cl26464
    Location:36 → 100
    Atrophin-1; Atrophin-1 family

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

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    146192335..146251105 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005247655.3 → XP_005247712.1  phospholipid scramblase 4 isoform X1

    See identical proteins and their annotated locations for XP_005247712.1

    UniProtKB/Swiss-Prot
    A8K2E9, Q2TTR3, Q658L3, Q6ZR73, Q7Z505, Q9NRQ2
    UniProtKB/TrEMBL
    B2R720
    Conserved Domains (2) summary
    pfam03803
    Location:100 → 322
    Scramblase; Scramblase
    cl26464
    Location:36 → 100
    Atrophin-1; Atrophin-1 family

  2. XM_017006921.2 → XP_016862410.1  phospholipid scramblase 4 isoform X2

    UniProtKB/TrEMBL
    E9PHR9
    Conserved Domains (2) summary
    cl02043
    Location:103 → 232
    LOR; LURP-one-related
    cl26464
    Location:36 → 152
    Atrophin-1; Atrophin-1 family

  3. XM_005247654.3 → XP_005247711.1  phospholipid scramblase 4 isoform X1

    See identical proteins and their annotated locations for XP_005247711.1

    UniProtKB/Swiss-Prot
    A8K2E9, Q2TTR3, Q658L3, Q6ZR73, Q7Z505, Q9NRQ2
    UniProtKB/TrEMBL
    B2R720
    Conserved Domains (2) summary
    pfam03803
    Location:100 → 322
    Scramblase; Scramblase
    cl26464
    Location:36 → 100
    Atrophin-1; Atrophin-1 family

  4. XM_047448623.1 → XP_047304579.1  phospholipid scramblase 4 isoform X2

    UniProtKB/TrEMBL
    E9PHR9

  5. XM_024453686.2 → XP_024309454.1  phospholipid scramblase 4 isoform X1

    UniProtKB/Swiss-Prot
    A8K2E9, Q2TTR3, Q658L3, Q6ZR73, Q7Z505, Q9NRQ2
    UniProtKB/TrEMBL
    B2R720
    Conserved Domains (2) summary
    pfam03803
    Location:100 → 322
    Scramblase; Scramblase
    cl26464
    Location:36 → 100
    Atrophin-1; Atrophin-1 family

  6. XM_024453687.2 → XP_024309455.1  phospholipid scramblase 4 isoform X2

    UniProtKB/TrEMBL
    E9PHR9
    Conserved Domains (2) summary
    cl02043
    Location:103 → 232
    LOR; LURP-one-related
    cl26464
    Location:36 → 152
    Atrophin-1; Atrophin-1 family

  7. XM_011513031.3 → XP_011511333.1  phospholipid scramblase 4 isoform X1

    See identical proteins and their annotated locations for XP_011511333.1

    UniProtKB/Swiss-Prot
    A8K2E9, Q2TTR3, Q658L3, Q6ZR73, Q7Z505, Q9NRQ2
    UniProtKB/TrEMBL
    B2R720
    Conserved Domains (2) summary
    pfam03803
    Location:100 → 322
    Scramblase; Scramblase
    cl26464
    Location:36 → 100
    Atrophin-1; Atrophin-1 family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    148947862..149006253 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347346.1 → XP_054203321.1  phospholipid scramblase 4 isoform X1

  2. XM_054347349.1 → XP_054203324.1  phospholipid scramblase 4 isoform X2

  3. XM_054347345.1 → XP_054203320.1  phospholipid scramblase 4 isoform X1

  4. XM_054347351.1 → XP_054203326.1  phospholipid scramblase 4 isoform X2

  5. XM_054347350.1 → XP_054203325.1  phospholipid scramblase 4 isoform X2

  6. XM_054347348.1 → XP_054203323.1  phospholipid scramblase 4 isoform X1

  7. XM_054347347.1 → XP_054203322.1  phospholipid scramblase 4 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NRQ2.2 GenPept UniProtKB/Swiss-Prot:Q9NRQ2

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