PRKRA protein activator of interferon induced protein kinase EIF2AK2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PRKRAprovided by HGNC
Official Full Name: protein activator of interferon induced protein kinase EIF2AK2provided by HGNC
Primary source: HGNC:HGNC:9438
See related: Ensembl:ENSG00000180228 MIM:603424; AllianceGenome:HGNC:9438
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: RAX; PACT; DYT16; HSD14
Summary: This gene encodes a protein kinase activated by double-stranded RNA which mediates the effects of interferon in response to viral infection. Mutations in this gene have been associated with dystonia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2008]
Expression: Ubiquitous expression in testis (RPKM 15.5), endometrium (RPKM 12.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q31.2

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (178431414..178451175, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (178914206..178933968, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (179296141..179315902, complement)

Chromosome 2 - NC_000002.12 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 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?

CRISPR Screen Reveals PACT as a Pro-Viral Factor for Dengue Viral Replication.
Title: CRISPR Screen Reveals PACT as a Pro-Viral Factor for Dengue Viral Replication.
PACT inhibits the replication of SARS-CoV-2 through the blockage of GSK-3beta-N-nsp3 cascade.
Title: PACT inhibits the replication of SARS-CoV-2 through the blockage of GSK-3β-N-nsp3 cascade.
PACT promotes the metastasis of basal-like breast cancer through Rac1 SUMOylation and activation.
Title: PACT promotes the metastasis of basal-like breast cancer through Rac1 SUMOylation and activation.
DYT-PRKRA Mutation P222L Enhances PACT's Stimulatory Activity on Type I Interferon Induction.
Title: DYT-PRKRA Mutation P222L Enhances PACT's Stimulatory Activity on Type I Interferon Induction.
SARS-CoV-2 NSP5 and N protein counteract the RIG-I signaling pathway by suppressing the formation of stress granules.
Title: SARS-CoV-2 NSP5 and N protein counteract the RIG-I signaling pathway by suppressing the formation of stress granules.
A tale of two proteins: PACT and PKR and their roles in inflammation.
Title: A tale of two proteins: PACT and PKR and their roles in inflammation.
High-throughput kinome-RNAi screen identifies protein kinase R activator (PACT) as a novel genetic modifier of CUG foci integrity in myotonic dystrophy type 1 (DM1).
Title: High-throughput kinome-RNAi screen identifies protein kinase R activator (PACT) as a novel genetic modifier of CUG foci integrity in myotonic dystrophy type 1 (DM1).
Dystonia 16 (DYT16) mutations in PACT cause dysregulated PKR activation and eIF2alpha signaling leading to a compromised stress response.
Title: Dystonia 16 (DYT16) mutations in PACT cause dysregulated PKR activation and eIF2α signaling leading to a compromised stress response.
Opposite actions of two dsRNA-binding proteins PACT and TRBP on RIG-I mediated signaling.
Title: Opposite actions of two dsRNA-binding proteins PACT and TRBP on RIG-I mediated signaling.
A truncated PACT protein resulting from a frameshift mutation reported in movement disorder DYT16 triggers caspase activation and apoptosis.
Title: A truncated PACT protein resulting from a frameshift mutation reported in movement disorder DYT16 triggers caspase activation and apoptosis.

Submit: New GeneRIF Correction See all GeneRIFs (64)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Dystonia 16 MedGen: C2677567 OMIM: 612067 GeneReviews: Hereditary Dystonia Overview	not available

EBI GWAS Catalog

Description
Oligoclonal band status in Scandinavian multiple sclerosis patients is associated with specific genetic risk alleles. 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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Protein interactions

Protein	Gene	Interaction	Pubs
Rev	rev	HIV-1 Rev binds TRBP/PACT complex and the binding requires the arginine rich motif (residues 35-50) of HIV-1 Rev	PubMed
Tat	tat	HIV-1 Tat binds TRBP/PACT complex and the binding requires the arginine rich motif (residues 48-58) of HIV-1 Tat	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

RH65973 (e-PCR)
- UniSTS:53510

RH103045 (e-PCR)
- UniSTS:97379

G20228 (e-PCR)
- UniSTS:60790

A005A41 (e-PCR)
- UniSTS:60791

RH16629 (e-PCR)
- UniSTS:61059

D2S1579E (e-PCR)
- UniSTS:150663

SGC32052 (e-PCR)
- UniSTS:3812

RH47285 (e-PCR)
- UniSTS:86244

G20590 (e-PCR)
- UniSTS:56815

A005Y08 (e-PCR)
- UniSTS:56816

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables double-stranded RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables double-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables enzyme activator activity	TAS Traceable Author Statement more info	PubMed
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables pre-miRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase activator activity	IDA Inferred from Direct Assay more info	PubMed
enables siRNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in RISC complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in antiviral innate immune response	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to oxidative stress	IEA Inferred from Electronic Annotation more info
involved_in immune response	TAS Traceable Author Statement more info	PubMed
involved_in miRNA processing	IDA Inferred from Direct Assay more info	PubMed
involved_in middle ear morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell population proliferation	TAS Traceable Author Statement more info	PubMed
involved_in outer ear morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of intrinsic apoptotic signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in pre-miRNA processing	IDA Inferred from Direct Assay more info	PubMed
involved_in protein stabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of regulatory ncRNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to virus	TAS Traceable Author Statement more info	PubMed
involved_in siRNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in siRNA processing	IDA Inferred from Direct Assay more info	PubMed
involved_in skeletal system morphogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of RISC complex	IBA Inferred from Biological aspect of Ancestor more info
part_of RISC-loading complex	IBA Inferred from Biological aspect of Ancestor more info
part_of RISC-loading complex	IDA Inferred from Direct Assay more info	PubMed
part_of RISC-loading complex	IPI Inferred from Physical Interaction more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasm	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
located_in cytosol	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: interferon-inducible double-stranded RNA-dependent protein kinase activator A

Names: PKR-associated protein X; PKR-associating protein X; protein activator of the interferon-induced protein kinase; protein kinase, interferon-inducible double-stranded RNA-dependent activator

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.

Genomic

NG_009053.1 RefSeqGene

Range

5057..24818

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001139517.1 → NP_001132989.1 interferon-inducible double-stranded RNA-dependent protein kinase activator A isoform 2

See identical proteins and their annotated locations for NP_001132989.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. This difference causes translation initiation at a downstream AUG and an isoform (2) with a shorter N-terminus compared to isoform 1.

Source sequence(s)

AC009948, AL833867

Consensus CDS

CCDS46460.1

UniProtKB/Swiss-Prot

O75569

Related

ENSP00000393883.2, ENST00000432031.6

Conserved Domains (2) summary

smart00358
Location:24 → 89

DSRM; Double-stranded RNA binding motif

cd00048
Location:115 → 181

DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
NM_001139518.1 → NP_001132990.1 interferon-inducible double-stranded RNA-dependent protein kinase activator A isoform 3

See identical proteins and their annotated locations for NP_001132990.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. This difference causes translation initiation at a downstream AUG and an isoform (3) with a shorter N-terminus compared to isoform 1.

Source sequence(s)

AC009948, AY251164

Consensus CDS

CCDS46461.1

UniProtKB/Swiss-Prot

O75569

Related

ENSP00000430604.1, ENST00000487082.5

Conserved Domains (3) summary

cd19889
Location:7 → 77

DSRM_PRKRA_rpt1; first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins

cd19891
Location:101 → 167

DSRM_PRKRA_rpt2; second double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins

cd19892
Location:214 → 285

DSRM_PRKRA_rpt3; third double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins
NM_001316362.2 → NP_001303291.1 interferon-inducible double-stranded RNA-dependent protein kinase activator A isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains an alternate exon compared to variant 1. This difference causes translation initiation at a downstream AUG and results in an isoform (4) with a shorter N-terminus compared to isoform 1.

Source sequence(s)

AA084317, AK296019, HY049565

Consensus CDS

CCDS92908.1

UniProtKB/TrEMBL

B4DJC7

Related

ENSP00000504030.1, ENST00000678775.1

Conserved Domains (2) summary

cd19891
Location:13 → 79

DSRM_PRKRA_rpt2; second double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins

cd19892
Location:126 → 197

DSRM_PRKRA_rpt3; third double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins
NM_003690.5 → NP_003681.1 interferon-inducible double-stranded RNA-dependent protein kinase activator A isoform 1

See identical proteins and their annotated locations for NP_003681.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AC009948, AK290601, BG827125

Consensus CDS

CCDS2279.1

UniProtKB/Swiss-Prot

A8K3I6, O75569, Q53G24, Q6X7T5, Q8NDK4

Related

ENSP00000318176.4, ENST00000325748.9

Conserved Domains (3) summary

cd19889
Location:32 → 102

DSRM_PRKRA_rpt1; first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins

cd19891
Location:126 → 192

DSRM_PRKRA_rpt2; second double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins

cd19892
Location:239 → 310

DSRM_PRKRA_rpt3; third double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

178431414..178451175 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011512063.3 → XP_011510365.1 interferon-inducible double-stranded RNA-dependent protein kinase activator A isoform X2

See identical proteins and their annotated locations for XP_011510365.1

UniProtKB/TrEMBL

A0A7I2V2I8

Related

ENSP00000502919.1, ENST00000677689.1

Conserved Domains (2) summary

cd19891
Location:41 → 107

DSRM_PRKRA_rpt2; second double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins

cd19892
Location:154 → 225

DSRM_PRKRA_rpt3; third double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins
XM_047446138.1 → XP_047302094.1 interferon-inducible double-stranded RNA-dependent protein kinase activator A isoform X1

UniProtKB/TrEMBL

A0A7I2V5H3

Related

ENSP00000504507.1, ENST00000677460.1

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

178914206..178933968 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054344302.1 → XP_054200277.1 interferon-inducible double-stranded RNA-dependent protein kinase activator A isoform X2

UniProtKB/TrEMBL

A0A7I2V2I8
XM_054344303.1 → XP_054200278.1 interferon-inducible double-stranded RNA-dependent protein kinase activator A isoform X3

UniProtKB/TrEMBL

B4DJC7
XM_054344301.1 → XP_054200276.1 interferon-inducible double-stranded RNA-dependent protein kinase activator A isoform X1

UniProtKB/TrEMBL

A0A7I2V5H3