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

Gene ID: 3475, updated on 12-Aug-2018

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; Vega:OTTHUMG00000155124
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

Genomic context

See IFRD1 in Genome Data Viewer
Location:
7q31.1
Exon count:
17
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 7 NC_000007.14 (112423144..112477940)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (112063199..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 uncharacterized LOC105375457 Neighboring gene leucine rich single-pass membrane protein 1 Neighboring gene nucleophosmin 1 pseudogene 14

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A meta-analysis of genome-wide association studies identifies novel variants associated with osteoarthritis of the hip.
NHGRI GWA Catalog
Age of onset of amyotrophic lateral sclerosis is modulated by a locus on 1p34.1.
NHGRI GWA 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.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

General protein information

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)

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
    5001..59060
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001007245.2NP_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
    O00458
    UniProtKB/TrEMBL
    A4D0U1
    Related
    ENSP00000005558.4, OTTHUMP00000207275, ENST00000005558.8, OTTHUMT00000338480
    Conserved Domains (2) summary
    pfam04836
    Location:392445
    IFRD_C; Interferon-related protein conserved region
    pfam05004
    Location:42346
    IFRD; Interferon-related developmental regulator (IFRD)
  2. NM_001197079.1NP_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/Swiss-Prot
    O00458
    Related
    ENSP00000439188.1, ENST00000535603.5
    Conserved Domains (2) summary
    pfam04836
    Location:342395
    IFRD_C; Interferon-related protein conserved region
    pfam05004
    Location:1296
    IFRD; Interferon-related developmental regulator (IFRD)
  3. NM_001197080.1NP_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, AK313211, AK315967, BF061555
    Consensus CDS
    CCDS56504.1
    UniProtKB/Swiss-Prot
    O00458
    Related
    ENSP00000483255.1, ENST00000621379.4
    Conserved Domains (2) summary
    pfam04836
    Location:342395
    IFRD_C; Interferon-related protein conserved region
    pfam05004
    Location:1296
    IFRD; Interferon-related developmental regulator (IFRD)
  4. NM_001550.3NP_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, BC001272, BF061555, BX648799, DC352698
    Consensus CDS
    CCDS34736.1
    UniProtKB/Swiss-Prot
    O00458
    UniProtKB/TrEMBL
    A4D0U1
    Related
    ENSP00000384477.3, OTTHUMP00000207380, ENST00000403825.7, OTTHUMT00000338700
    Conserved Domains (2) summary
    pfam04836
    Location:392445
    IFRD_C; Interferon-related protein conserved region
    pfam05004
    Location:42346
    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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p12 Primary Assembly

    Range
    112423144..112477940
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011516142.3XP_011514444.1  interferon-related developmental regulator 1 isoform X1

    Conserved Domains (2) summary
    pfam04836
    Location:397450
    IFRD_C; Interferon-related protein conserved region
    pfam05004
    Location:42351
    IFRD; Interferon-related developmental regulator (IFRD)
  2. XM_011516143.3XP_011514445.1  interferon-related developmental regulator 1 isoform X2

    Conserved Domains (2) summary
    pfam04836
    Location:347400
    IFRD_C; Interferon-related protein conserved region
    pfam05004
    Location:1301
    IFRD; Interferon-related developmental regulator (IFRD)

RNA

  1. XR_927462.3 RNA Sequence

  2. XR_001744704.2 RNA Sequence

  3. XR_001744703.2 RNA Sequence

  4. XR_927463.3 RNA Sequence

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