Irf5 interferon regulatory factor 5 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Irf5provided by RGD
Official Full Name: interferon regulatory factor 5provided by RGD
Primary source: RGD:1310447
See related: EnsemblRapid:ENSRNOG00000007437 AllianceGenome:RGD:1310447
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
Summary: Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and identical protein binding activity. Predicted to be involved in several processes, including positive regulation of macromolecule biosynthetic process; response to peptidoglycan; and response to virus. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Biomarker of obstructive jaundice and ureteral obstruction. Human ortholog(s) of this gene implicated in herpes simplex; inflammatory bowel disease 14; multiple sclerosis; rheumatoid arthritis; and systemic lupus erythematosus. Orthologous to human IRF5 (interferon regulatory factor 5). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Spleen (RPKM 111.6), Thymus (RPKM 32.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q22

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (59092914..59104596)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (58127577..58140665)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (56804477..56816271)

Chromosome 4 - NC_086022.1 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: 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?

Mechanism of IRF5-regulated CXCL13/CXCR5 Signaling Axis in CCI-induced Neuropathic Pain in Rats.
Title: Mechanism of IRF5-regulated CXCL13/CXCR5 Signaling Axis in CCI-induced Neuropathic Pain in Rats.
Depression Exacerbates Dextran Sulfate Sodium-Induced Colitis via IRF5-Mediated Macrophage Polarization.
Title: Depression Exacerbates Dextran Sulfate Sodium-Induced Colitis via IRF5-Mediated Macrophage Polarization.
BoDV-1 infection induces neuroinflammation by activating the TLR4/MyD88/IRF5 signaling pathway, leading to learning and memory impairment in rats.
Title: BoDV-1 infection induces neuroinflammation by activating the TLR4/MyD88/IRF5 signaling pathway, leading to learning and memory impairment in rats.
Bone marrow mesenchymal stem cell-derived exosomal microRNA-125a promotes M2 macrophage polarization in spinal cord injury by downregulating IRF5.
Title: Bone marrow mesenchymal stem cell-derived exosomal microRNA-125a promotes M2 macrophage polarization in spinal cord injury by downregulating IRF5.
MicroRNA-22-3p alleviates spinal cord ischemia/reperfusion injury by modulating M2 macrophage polarization via IRF5.
Title: MicroRNA-22-3p alleviates spinal cord ischemia/reperfusion injury by modulating M2 macrophage polarization via IRF5.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cellular response to virus	ISO Inferred from Sequence Orthology more info
involved_in cytokine-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in defense response to virus	ISO Inferred from Sequence Orthology more info
involved_in immune system process	IBA Inferred from Biological aspect of Ancestor more info
involved_in innate immune response	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cytokine production involved in immune response	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of type I interferon production	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to muramyl dipeptide	ISO Inferred from Sequence Orthology more info
involved_in response to peptidoglycan	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: interferon regulatory factor 5

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_001106586.1 → NP_001100056.1 interferon regulatory factor 5

See identical proteins and their annotated locations for NP_001100056.1

Status: PROVISIONAL

Source sequence(s)

CH473959

UniProtKB/TrEMBL

A0A8I5YBA0, A6IEE2, D3ZPU1

Related

ENSRNOP00000069195.3, ENSRNOT00000085483.3

Conserved Domains (2) summary

pfam00605
Location:16 → 121

IRF; Interferon regulatory factor transcription factor

pfam10401
Location:247 → 430

IRF-3; Interferon-regulatory factor 3

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086022.1 Reference GRCr8

Range

59092914..59104596

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_008762765.4 → XP_008760987.1 interferon regulatory factor 5 isoform X4

See identical proteins and their annotated locations for XP_008760987.1

UniProtKB/TrEMBL

A0A8I5YBA0

Conserved Domains (2) summary

pfam00605
Location:16 → 121

IRF; Interferon regulatory factor transcription factor

pfam10401
Location:251 → 434

IRF-3; Interferon-regulatory factor 3
XM_063285738.1 → XP_063141808.1 interferon regulatory factor 5 isoform X3

UniProtKB/TrEMBL

A0A8I5YBA0

Related

ENSRNOP00000109028.1, ENSRNOT00000135232.1
XM_039107277.2 → XP_038963205.1 interferon regulatory factor 5 isoform X1

UniProtKB/TrEMBL

A0A0G2JUR2, A0A8I5YBA0

Conserved Domains (2) summary

pfam00605
Location:43 → 148

IRF; Interferon regulatory factor transcription factor

pfam10401
Location:278 → 461

IRF-3; Interferon-regulatory factor 3
XM_006236184.5 → XP_006236246.1 interferon regulatory factor 5 isoform X4

See identical proteins and their annotated locations for XP_006236246.1

UniProtKB/TrEMBL

A0A8I5YBA0

Related

ENSRNOP00000100832.1, ENSRNOT00000168534.1

Conserved Domains (2) summary

pfam00605
Location:16 → 121

IRF; Interferon regulatory factor transcription factor

pfam10401
Location:251 → 434

IRF-3; Interferon-regulatory factor 3
XM_006236185.5 → XP_006236247.1 interferon regulatory factor 5 isoform X4

See identical proteins and their annotated locations for XP_006236247.1

UniProtKB/TrEMBL

A0A8I5YBA0

Conserved Domains (2) summary

pfam00605
Location:16 → 121

IRF; Interferon regulatory factor transcription factor

pfam10401
Location:251 → 434

IRF-3; Interferon-regulatory factor 3
XM_039107278.2 → XP_038963206.1 interferon regulatory factor 5 isoform X2

UniProtKB/TrEMBL

A0A8I5YBA0

Related

ENSRNOP00000010001.6, ENSRNOT00000010001.8

Conserved Domains (2) summary

pfam00605
Location:25 → 130

IRF; Interferon regulatory factor transcription factor

pfam10401
Location:260 → 443

IRF-3; Interferon-regulatory factor 3