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

Summary

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: mouse all
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Genomic context

Location:: 7q31.1

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (112423174..112477203)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (113741458..113795506)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (112063229..112117258)

Chromosome 7 - NC_000007.14 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?

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.
IFRD1 regulates the asthmatic responses of airway via NF-kappaB pathway.
Title: IFRD1 regulates the asthmatic responses of airway via NF-κB pathway.
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.
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.
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.
rs7817 polymorphism associated with nasal polyposis in cystic fibrosis patients
Title: IFRD1 gene polymorphisms are associated with nasal polyposis in cystic fibrosis patients.
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.
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.
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.
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 EBI GWAS CatalogPubMed
Age of onset of amyotrophic lateral sclerosis is modulated by a locus on 1p34.1. EBI GWAS Catalog EBI GWAS CatalogPubMed
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 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH102966 (e-PCR)
- UniSTS:97300

SHGC-83988 (e-PCR)
- UniSTS:104553

G19708 (e-PCR)
- UniSTS:60787

A001W15 (e-PCR)
- UniSTS:60788

RH11542 (e-PCR)
- UniSTS:64725

G49165 (e-PCR)
- UniSTS:96220

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

NG_027799.1 RefSeqGene

Range

32317..59060

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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)
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)
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

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