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PLSCR4 phospholipid scramblase 4 [ Homo sapiens (human) ]

Gene ID: 57088, updated on 10-Dec-2019

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
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
Expression
Ubiquitous expression in fat (RPKM 22.0), gall bladder (RPKM 21.1) and 24 other tissues See more
Orthologs
mouse all

Genomic context

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See PLSCR4 in Genome Data Viewer
Location:
3q24
Exon count:
12
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (146192335..146251179, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (145910122..145968966, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 Neighboring gene uncharacterized LOC105374145 Neighboring gene phospholipid scramblase 4 pseudogene Neighboring gene phospholipid scramblase 2

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. Biochemical and functional characterization of human phospholipid scramblase 4 (hPLSCR4). Francis VG, et al. Biol Chem, 2012 Oct. PMID 23089641
  2. Snail represses the expression of human phospholipid scramblase 4 gene. Vinnakota JM, et al. Gene, 2016 Oct 15. PMID 27363667
  3. 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
  4. 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. Sahu SK, et al. Biochim Biophys Acta, 2009 Oct. PMID 19540310
  5. Identification of three new members of the phospholipid scramblase gene family. Wiedmer T, et al. Biochim Biophys Acta, 2000 Jul 31. PMID 10930526

See all (22) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. biochemical and functional characterization of human phospholipid scramblase 4
    Title: Biochemical and functional characterization of human phospholipid scramblase 4 (hPLSCR4).
  3. 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.
  4. 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.
  5. 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.
  6. SLPI is a ligand for PLSCR1 and PLSCR4, which also interact directly with the CD4 receptor at the cell surface of T lymphocytes
    Title: The phospholipid scramblases 1 and 4 are cellular receptors for the secretory leukocyte protease inhibitor and interact with CD4 at the plasma membrane.
Submit: New GeneRIF Correction

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

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
CD4 receptor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
SH3 domain binding IEA
Inferred from Electronic Annotation
more info
  
calcium ion binding NAS
Non-traceable Author Statement
more info
 PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
phospholipid scramblase activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
phospholipid scramblase activity NAS
Non-traceable Author Statement
more info
 PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
cellular response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
  
phospholipid scrambling IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
phospholipid scrambling NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
integral component of membrane IEA
Inferred from Electronic Annotation
more info
  
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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
    Q9NRQ2
    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
    Q9NRQ2
    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_001128306.1 → 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/Swiss-Prot
    Q9NRQ2
    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
    Q9NRQ2
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    146192335..146251179 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017006921.1 → 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

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

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

  3. XM_005247654.2 → XP_005247711.1  phospholipid scramblase 4 isoform X1

    See identical proteins and their annotated locations for XP_005247711.1

    UniProtKB/Swiss-Prot
    Q9NRQ2
    Conserved Domains (2) summary
    pfam03803
    Location:100 → 322
    Scramblase; Scramblase
    cl26464
    Location:36 → 100
    Atrophin-1; Atrophin-1 family

  4. XM_005247655.2 → XP_005247712.1  phospholipid scramblase 4 isoform X1

    See identical proteins and their annotated locations for XP_005247712.1

    UniProtKB/Swiss-Prot
    Q9NRQ2
    Conserved Domains (2) summary
    pfam03803
    Location:100 → 322
    Scramblase; Scramblase
    cl26464
    Location:36 → 100
    Atrophin-1; Atrophin-1 family

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

    Conserved Domains (2) summary
    pfam03803
    Location:100 → 322
    Scramblase; Scramblase
    cl26464
    Location:36 → 100
    Atrophin-1; Atrophin-1 family

  6. XM_011513031.2 → XP_011511333.1  phospholipid scramblase 4 isoform X1

    See identical proteins and their annotated locations for XP_011511333.1

    UniProtKB/Swiss-Prot
    Q9NRQ2
    Conserved Domains (2) summary
    pfam03803
    Location:100 → 322
    Scramblase; Scramblase
    cl26464
    Location:36 → 100
    Atrophin-1; Atrophin-1 family
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NRQ2.2 GenPept UniProtKB/Swiss-Prot:Q9NRQ2

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