PLSCR4 phospholipid scramblase 4 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: 3q24

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (146192335..146251105, complement)
110	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_000003.12 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?

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.
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.
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.
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.
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.
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.
biochemical and functional characterization of human phospholipid scramblase 4
Title: Biochemical and functional characterization of human phospholipid scramblase 4 (hPLSCR4).
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Homologs of the PLSCR4 gene: The PLSCR4 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, and rat.
Orthologs from Annotation Pipeline: 169 organisms have orthologs with human gene PLSCR4
Orthologs

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	PubMed
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	PubMed
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	PubMed
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)

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

Q7Z505, 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
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

Q7Z505, 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
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/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
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
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

Q7Z505, 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 Annotation Release 110 details...

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

146192335..146251105 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Q7Z505, Q9NRQ2

Conserved Domains (2) summary

pfam03803
Location:100 → 322

Scramblase; Scramblase

cl26464
Location:36 → 100

Atrophin-1; Atrophin-1 family
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
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

Q7Z505, Q9NRQ2

Conserved Domains (2) summary

pfam03803
Location:100 → 322

Scramblase; Scramblase

cl26464
Location:36 → 100

Atrophin-1; Atrophin-1 family
XM_047448623.1 → XP_047304579.1 phospholipid scramblase 4 isoform X2

UniProtKB/TrEMBL

E9PHR9
XM_024453686.2 → XP_024309454.1 phospholipid scramblase 4 isoform X1

UniProtKB/Swiss-Prot

Q7Z505

Conserved Domains (2) summary

pfam03803
Location:100 → 322

Scramblase; Scramblase

cl26464
Location:36 → 100

Atrophin-1; Atrophin-1 family
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
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

Q7Z505, Q9NRQ2

Conserved Domains (2) summary

pfam03803
Location:100 → 322

Scramblase; Scramblase

cl26464
Location:36 → 100

Atrophin-1; Atrophin-1 family