Prf1 perforin 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Prf1provided by RGD
Official Full Name: perforin 1provided by RGD
Primary source: RGD:708463
See related: EnsemblRapid:ENSRNOG00000000562 AllianceGenome:RGD:708463
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Cyta; RATCYTA
Summary: Predicted to enable calcium ion binding activity; identical protein binding activity; and wide pore channel activity. Involved in apoptotic process; circadian rhythm; and response to ethanol. Located in cytoplasmic vesicle and extracellular space. Used to study asthma; colon carcinoma; and glomerulonephritis. Biomarker of membranoproliferative glomerulonephritis. Human ortholog(s) of this gene implicated in several diseases, including Crohn's disease; familial hemophagocytic lymphohistiocytosis 2; human immunodeficiency virus infectious disease; multiple sclerosis; and non-Langerhans-cell histiocytosis. Orthologous to human PRF1 (perforin 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 311.8), Lung (RPKM 246.6) and 5 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20q11

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (29789040..29794550)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (29246202..29251712)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (30915294..30920804)

Chromosome 20 - NC_086038.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Defining the interaction of perforin with calcium and the phospholipid membrane.
Title: Defining the interaction of perforin with calcium and the phospholipid membrane.
Hypomethylation of perforin regulatory elements in CD4+ T cells may result in the lung septal cell apoptosis associated with the development of experimental autoimmune emphysema
Title: Hypomethylation of perforin regulatory elements in CD4+ T cells from rat spleens contributes to the development of autoimmune emphysema.
Perforin and GzmB may play important roles in the pathogenesis of asthma.
Title: [Expression of perforin and granzyme B in asthmatic rats and intervention of recombinant human growth hormone].
In early stage of acute rejection of renal allograft in rats, the expressions of osteopontin, IL15, perforin and granzyme B are up-regulated.
Title: [Expressions of interleukin-15 and osteopontin mRNA in early stage of acute rejection of renal allograft in rats].
In antiglomerular basement membrane crescentic glomerulonephritis, glomerular mRNA expression of perforin and granzyme B corresponded with the number of CD8+ cells, whereas that of granzyme A, Fas, and FasL did not.
Title: Anti-perforin antibody treatment ameliorates experimental crescentic glomerulonephritis in WKY rats.
the perforin C2 domain regulates calcium-dependent plasma membrane binding and cell lysis
Title: Calcium-dependent plasma membrane binding and cell lysis by perforin are mediated through its C2 domain: A critical role for aspartate residues 429, 435, 483, and 485 but not 491.
The protein level of perforin follows a physiological circadian rhythm in rat splenocytes that concurrently drives the circadian rhythm of natural killer cell cytolytic activity.
Title: Circadian rhythms of granzyme B, perforin, IFN-gamma, and NK cell cytolytic activity in the spleen: effects of chronic ethanol.
a systematic functional analysis of hemophagocytic lymphohistiocytosis-associated missense mutations and the two most common perforin polymorphisms
Title: A functional analysis of the putative polymorphisms A91V and N252S and 22 missense perforin mutations associated with familial hemophagocytic lymphohistiocytosis.

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General gene information

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Markers

AU028895 (e-PCR)
- UniSTS:111888

d20rat27 (e-PCR)
- UniSTS:121541

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables calcium ion binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables pore-forming activity	IEA Inferred from Electronic Annotation more info
enables wide pore channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables wide pore channel activity	IEA Inferred from Electronic Annotation more info
enables wide pore channel activity	ISO Inferred from Sequence Orthology more info
enables wide pore channel activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in T cell mediated cytotoxicity	IBA Inferred from Biological aspect of Ancestor more info
involved_in T cell mediated cytotoxicity	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within T cell mediated cytotoxicity	ISO Inferred from Sequence Orthology more info
involved_in T cell mediated cytotoxicity	ISO Inferred from Sequence Orthology more info
involved_in circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in defense response to tumor cell	IEA Inferred from Electronic Annotation more info
involved_in defense response to tumor cell	ISO Inferred from Sequence Orthology more info
involved_in defense response to tumor cell	ISS Inferred from Sequence or Structural Similarity more info
involved_in defense response to virus	IBA Inferred from Biological aspect of Ancestor more info
involved_in defense response to virus	IEA Inferred from Electronic Annotation more info
involved_in defense response to virus	ISO Inferred from Sequence Orthology more info
involved_in defense response to virus	ISS Inferred from Sequence or Structural Similarity more info
involved_in granzyme-mediated programmed cell death signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in granzyme-mediated programmed cell death signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in immune response to tumor cell	IEA Inferred from Electronic Annotation more info
involved_in immune response to tumor cell	ISO Inferred from Sequence Orthology more info
involved_in immune response to tumor cell	ISS Inferred from Sequence or Structural Similarity more info
involved_in immunological synapse formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in immunological synapse formation	IEA Inferred from Electronic Annotation more info
involved_in immunological synapse formation	ISO Inferred from Sequence Orthology more info
involved_in killing of cells of another organism	IEA Inferred from Electronic Annotation more info
involved_in leukocyte mediated cytotoxicity	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of killing of cells of another organism	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of killing of cells of another organism	ISO Inferred from Sequence Orthology more info
involved_in protein homooligomerization	IEA Inferred from Electronic Annotation more info
involved_in protein homooligomerization	ISO Inferred from Sequence Orthology more info
involved_in protein homooligomerization	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein import	IEA Inferred from Electronic Annotation more info
involved_in protein import	ISO Inferred from Sequence Orthology more info
involved_in protein secretion	IEA Inferred from Electronic Annotation more info
involved_in protein secretion	ISO Inferred from Sequence Orthology more info
involved_in protein transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in protein transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in response to ethanol	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in cytolytic granule	IEA Inferred from Electronic Annotation more info
located_in cytolytic granule	ISO Inferred from Sequence Orthology more info
located_in cytolytic granule	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasmic vesicle	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic vesicle	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in endosome lumen	IEA Inferred from Electronic Annotation more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in immunological synapse	IEA Inferred from Electronic Annotation more info
is_active_in immunological synapse	ISO Inferred from Sequence Orthology more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in membrane	ISO Inferred from Sequence Orthology more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: perforin-1

Names: P1; cytolysin; lymphocyte pore-forming protein; perforin 1 (pore forming protein)

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_017330.2 → NP_059026.2 perforin-1 precursor

See identical proteins and their annotated locations for NP_059026.2

Status: PROVISIONAL

Source sequence(s)

BC089808

UniProtKB/Swiss-Prot

P35763

UniProtKB/TrEMBL

Q5FVS5

Related

ENSRNOP00000078379.1, ENSRNOT00000100131.2

Conserved Domains (2) summary

cd04032
Location:387 → 513

C2_Perforin; C2 domain of Perforin

smart00457
Location:166 → 368

MACPF; membrane-attack complex / perforin