irf1a interferon regulatory factor 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: irf1aprovided by ZNC
Official Full Name: interferon regulatory factor 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-060421-4031
See related: Ensembl:ENSDARG00000043492 AllianceGenome:ZFIN:ZDB-GENE-060421-4031
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: irf1; IRF11; zgc:136945
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in immune system process and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of DNA-templated transcription. Predicted to be active in nucleus. Is expressed in several structures, including blood; digestive system; eye; immune system; and integument. Human ortholog(s) of this gene implicated in asthma; lung cancer (multiple); primary immunodeficiency disease; smallpox; and stomach cancer (multiple). Orthologous to human IRF1 (interferon regulatory factor 1). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 13

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	13	NC_007124.7 (311380..318828)
105	previous assembly	GRCz10 (GCF_000002035.5)	13	NC_007124.6 (181153..188746)

Chromosome 13 - NC_007124.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Characterization of DNA Binding and Nuclear Retention Identifies Zebrafish IRF11 as a Positive Regulator of IFN Antiviral Response.
Title: Characterization of DNA Binding and Nuclear Retention Identifies Zebrafish IRF11 as a Positive Regulator of IFN Antiviral Response.
Following spring viremia of carp virus infection, DrIFNPhi1/3 and DrIRF1/3/7 transcripts are significantly induced in zebrafish tissues, which correlates with the replication of spring viremia of carp virus. data provide evidence that fish and mammals have evolved a similar IRF-dependent regulatory mechanism fine-tuning IFN gene activation.
Title: Zebrafish IRF1, IRF3, and IRF7 Differentially Regulate IFNΦ1 and IFNΦ3 Expression through Assembly of Homo- or Heteroprotein Complexes.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables transcription cis-regulatory region binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in immune system process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: interferon regulatory factor 1a

Names: interferon regulatory factor 1

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_001040352.1 → NP_001035442.1 interferon regulatory factor 1a

See identical proteins and their annotated locations for NP_001035442.1

Status: PROVISIONAL

Source sequence(s)

BC115340

UniProtKB/TrEMBL

Q1RLP9

Related

ENSDARP00000070128.3, ENSDART00000075646.4

Conserved Domains (1) summary

pfam00605
Location:7 → 112

IRF; Interferon regulatory factor transcription factor

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007124.7 Reference GRCz11 Primary Assembly

Range

311380..318828

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009307024.4 → XP_009305299.1 interferon regulatory factor 1a isoform X1

UniProtKB/TrEMBL

A0A8M3AYR2

Conserved Domains (1) summary

pfam00605
Location:7 → 112

IRF; Interferon regulatory factor transcription factor