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IFRD1 interferon related developmental regulator 1 [ Homo sapiens (human) ]

Gene ID: 3475, updated on 5-Mar-2024

Summary

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Official Symbol
IFRD1provided by HGNC
Official Full Name
interferon related developmental regulator 1provided by HGNC
Primary source
HGNC:HGNC:5456
See related
Ensembl:ENSG00000006652 MIM:603502; AllianceGenome:HGNC:5456
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
PC4; TIS7
Summary
This gene is an immediate early gene that encodes a protein related to interferon-gamma. This protein may function as a transcriptional co-activator/repressor that controls the growth and differentiation of specific cell types during embryonic development and tissue regeneration. Mutations in this gene are associated with sensory/motor neuropathy with ataxia. This gene may also be involved in modulating the pathogenesis of cystic fibrosis lung disease. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2010]
Expression
Ubiquitous expression in bone marrow (RPKM 30.1), pancreas (RPKM 9.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
7q31.1
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (112423174..112477203)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (113741458..113795506)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (112063229..112117258)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375456 Neighboring gene MT-ND6 pseudogene 24 Neighboring gene MT-CYB pseudogene 24 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:112032323-112032832 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:112055185-112055686 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:112055687-112056186 Neighboring gene uncharacterized LOC105375457 Neighboring gene Sharpr-MPRA regulatory region 10411 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:112089605-112090422 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:112090423-112091240 Neighboring gene uncharacterized LOC128031837 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26513 Neighboring gene leucine rich single-pass membrane protein 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:112136767-112136980 Neighboring gene nucleophosmin 1 pseudogene 14

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Increased IFRD1 Expression in Human Colon Cancers Predicts Reduced Patient Survival. Lewis MA, et al. Dig Dis Sci, 2017 Dec. PMID 29094309, Free PMC Article
  2. IFRD1 gene polymorphisms are associated with nasal polyposis in cystic fibrosis patients. Baldan A, et al. Rhinology, 2015 Dec. PMID 26397160
  3. The interferon-related developmental regulator 1 is used by human papillomavirus to suppress NFκB activation. Tummers B, et al. Nat Commun, 2015 Mar 13. PMID 26055519, Free PMC Article
  4. IFRD1 polymorphisms and gastric cancer risk in a Chinese population. Xu R, et al. Med Oncol, 2014 Sep. PMID 25073439
  5. Expression and regulation of interferon-related development regulator-1 in cystic fibrosis neutrophils. Hector A, et al. Am J Respir Cell Mol Biol, 2013 Jan. PMID 23043087

See all (70) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Insights on the disruption of the complex between human positive coactivator 4 and p53 by small molecules.
    Title: Insights on the disruption of the complex between human positive coactivator 4 and p53 by small molecules.
  2. IFRD1 regulates the asthmatic responses of airway via NF-kappaB pathway.
    Title: IFRD1 regulates the asthmatic responses of airway via NF-κB pathway.
  3. Results from a study on gene expression variability markers in early-stage human embryos shows that IFRD1 is a putative marker for the 3-day, 8-cell embryo stage.
    Title: Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
  4. High IFRD1 colon cancer expression was significantly associated with decreased 5-year patient survival.
    Title: Increased IFRD1 Expression in Human Colon Cancers Predicts Reduced Patient Survival.
  5. this study shows that IFRD1 gene may be associated with pathogenesis of asthma
    Title: Uncovering potential key genes associated with the pathogenesis of asthma: A microarray analysis of asthma-relevant tissues.
  6. rs7817 polymorphism associated with nasal polyposis in cystic fibrosis patients
    Title: IFRD1 gene polymorphisms are associated with nasal polyposis in cystic fibrosis patients.
  7. study reveals an EGFR-IFRD1-mediated viral immune evasion mechanism, which can also be exploited by cancer cells
    Title: The interferon-related developmental regulator 1 is used by human papillomavirus to suppress NFκB activation.
  8. rs5009270 may contribute to hip OA susceptibility by altering proximal femur shape.
    Title: Investigation of association between hip osteoarthritis susceptibility loci and radiographic proximal femur shape.
  9. PC4 plays essential roles in the transition step from transcription initiation to elongation by binding to melted DNA in collaboration with TFIIEbeta.
    Title: Transcription cofactor PC4 plays essential roles in collaboration with the small subunit of general transcription factor TFIIE.
  10. Studied the association between IFRD1 polymorphisms and gastric cancer in a Chinese population.
    Title: IFRD1 polymorphisms and gastric cancer risk in a Chinese population.
Submit: New GeneRIF Correction See all GeneRIFs (29)

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

EBI GWAS Catalog

Description
A meta-analysis of genome-wide association studies identifies novel variants associated with osteoarthritis of the hip.
EBI GWAS Catalog
Age of onset of amyotrophic lateral sclerosis is modulated by a locus on 1p34.1.
EBI GWAS Catalog
Genomic variation associated with mortality among adults of European and African ancestry with heart failure: the cohorts for heart and aging research in genomic epidemiology consortium.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in myoblast fate determination TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of axon extension IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of collateral sprouting IEA
Inferred from Electronic Annotation
more info
  
involved_in skeletal muscle tissue regeneration IEA
Inferred from Electronic Annotation
more info
  
involved_in striated muscle tissue development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in sarcoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
interferon-related developmental regulator 1
Names
12-O-tetradecanoylphorbol-13-acetate-induced sequence 7
TPA induced sequence 7
nerve growth factor-inducible protein PC4
pheochromocytoma cell-4

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

  1. NG_027799.1 RefSeqGene

    Range
    32317..59060
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001007245.3 → NP_001007246.1  interferon-related developmental regulator 1 isoform 1

    See identical proteins and their annotated locations for NP_001007246.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AC005192, AK313211, BF061555, BX648799
    Consensus CDS
    CCDS34736.1
    UniProtKB/Swiss-Prot
    B7Z5G1, O00458, O75234, Q5U013, Q9BVE4
    UniProtKB/TrEMBL
    A0A6Q8PHD2, A4D0U1
    Related
    ENSP00000005558.4, ENST00000005558.8
    Conserved Domains (2) summary
    pfam04836
    Location:392 → 445
    IFRD_C; Interferon-related protein conserved region
    pfam05004
    Location:42 → 346
    IFRD; Interferon-related developmental regulator (IFRD)

  2. NM_001197079.2 → NP_001184008.1  interferon-related developmental regulator 1 isoform 2

    See identical proteins and their annotated locations for NP_001184008.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1. Both variant 3 and 4 encode the same isoform (2).
    Source sequence(s)
    AC005192, AC079741, AK298894, BF061555, DC314572
    Consensus CDS
    CCDS56504.1
    UniProtKB/TrEMBL
    A0A6Q8PHD2
    Related
    ENSP00000439188.1, ENST00000535603.5
    Conserved Domains (2) summary
    pfam04836
    Location:342 → 395
    IFRD_C; Interferon-related protein conserved region
    pfam05004
    Location:1 → 296
    IFRD; Interferon-related developmental regulator (IFRD)

  3. NM_001197080.2 → NP_001184009.1  interferon-related developmental regulator 1 isoform 2

    See identical proteins and their annotated locations for NP_001184009.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1. Both variant 3 and 4 encode the same isoform (2).
    Source sequence(s)
    AC005192, AK315967, BF061555
    Consensus CDS
    CCDS56504.1
    UniProtKB/TrEMBL
    A0A6Q8PHD2
    Related
    ENSP00000483255.1, ENST00000621379.4
    Conserved Domains (2) summary
    pfam04836
    Location:342 → 395
    IFRD_C; Interferon-related protein conserved region
    pfam05004
    Location:1 → 296
    IFRD; Interferon-related developmental regulator (IFRD)

  4. NM_001550.4 → NP_001541.2  interferon-related developmental regulator 1 isoform 1

    See identical proteins and their annotated locations for NP_001541.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1). Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AC005192, AC079741
    Consensus CDS
    CCDS34736.1
    UniProtKB/Swiss-Prot
    B7Z5G1, O00458, O75234, Q5U013, Q9BVE4
    UniProtKB/TrEMBL
    A0A6Q8PHD2, A4D0U1
    Related
    ENSP00000384477.3, ENST00000403825.8
    Conserved Domains (2) summary
    pfam04836
    Location:392 → 445
    IFRD_C; Interferon-related protein conserved region
    pfam05004
    Location:42 → 346
    IFRD; Interferon-related developmental regulator (IFRD)

RNA

  1. NR_120333.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an internal exon in the 5' region and has an additional exon in the 3' region, compared to variant 1. This variant is represented as non-coding because use of the 5'-most expected translation start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC005192, AK297509, AK298894, BF061555, CN265021

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    112423174..112477203
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    113741458..113795506
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O00458.4 GenPept UniProtKB/Swiss-Prot:O00458

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