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    IFRD2 interferon related developmental regulator 2 [ Homo sapiens (human) ]

    Gene ID: 7866, updated on 5-Mar-2024

    Summary

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    Official Symbol
    IFRD2provided by HGNC
    Official Full Name
    interferon related developmental regulator 2provided by HGNC
    Primary source
    HGNC:HGNC:5457
    See related
    Ensembl:ENSG00000214706 MIM:602725; AllianceGenome:HGNC:5457
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SM15; IFNRP; SKMc15
    Summary
    Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in stomach (RPKM 16.0), thyroid (RPKM 14.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See IFRD2 in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (50287732..50292429, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (50317089..50321785, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (50325163..50329860, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SEMA3B antisense RNA 1 (head to head) Neighboring gene semaphorin 3B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19897 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50310784-50311307 Neighboring gene microRNA 6872 Neighboring gene leucine rich single-pass membrane protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50330739-50331294 Neighboring gene hyaluronidase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19899 Neighboring gene N-alpha-acetyltransferase 80, NatH catalytic subunit Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50340489-50341423 Neighboring gene hyaluronidase 1

    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. Structures of translationally inactive mammalian ribosomes. Brown A, et al. Elife, 2018 Oct 24. PMID 30355441, Free PMC Article
    2. The human homolog of the rodent immediate early response genes, PC4 and TIS7, resides in the lung cancer tumor suppressor gene region on chromosome 3p21. Latif F, et al. Hum Genet, 1997 Mar. PMID 9050919
    3. Cloning of the human interferon-related developmental regulator (IFRD1) gene coding for the PC4 protein, a member of a novel family of developmentally regulated genes. Buanne P, et al. Genomics, 1998 Jul 15. PMID 9722946
    4. Mechanism of client selection by the protein quality-control factor UBE2O. Yip MCJ, et al. Nat Struct Mol Biol, 2022 Aug. PMID 35915257, Free PMC Article
    5. The 630-kb lung cancer homozygous deletion region on human chromosome 3p21.3: identification and evaluation of the resident candidate tumor suppressor genes. The International Lung Cancer Chromosome 3p21.3 Tumor Suppressor Gene Consortium. Lerman MI, et al. Cancer Res, 2000 Nov 1. PMID 11085536

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of a new family of IFRD (interferon developmental regulator) genes, of which SkMC15 is part, being named IFDR2
      Title: Cloning of the human interferon-related developmental regulator (IFRD1) gene coding for the PC4 protein, a member of a novel family of developmentally regulated genes.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variation and antioxidant response gene expression in the bronchial airway epithelium of smokers at risk for lung cancer.
    3. Identification of the IFRD gene family, comprising the two genes PC4 / Tis7 / IFRD1 and SKMc15 / IFRD2, and in situ-hybridization analysis of their expression during developments
      Title: Cloning of the human interferon-related developmental regulator (IFRD1) gene coding for the PC4 protein, a member of a novel family of developmentally regulated genes.
    4. This publication discusses both IFRD1 and IFRD2.
      Title: Cloning of the human interferon-related developmental regulator (IFRD1) gene coding for the PC4 protein, a member of a novel family of developmentally regulated genes.
    Submit: New GeneRIF Correction

    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

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of interferon-related developmental regulator 2 (IFRD2) by siRNA has both activating and inhibiting activities on HIV-1 replication in HeLa P4/R5 cells, suggesting a regulatory role in HIV replication PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ40446

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ribosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables translation repressor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of translation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus HDA PubMed 

    General protein information

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    Preferred Names
    interferon-related developmental regulator 2
    Names
    interferon-related protein

    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)

    1. NM_006764.5 → NP_006755.5  interferon-related developmental regulator 2

      Status: VALIDATED

      Source sequence(s)
      U90094
      Consensus CDS
      CCDS77746.2
      UniProtKB/Swiss-Prot
      A0A0R4J2F6, Q12894, Q9BVB4, Q9UJ88
      UniProtKB/TrEMBL
      B3KQD7
      Related
      ENSP00000402849.4, ENST00000417626.8
      Conserved Domains (2) summary
      pfam04836
      Location:386 → 439
      IFRD_C; Interferon-related protein conserved region
      pfam05004
      Location:32 → 341
      IFRD; Interferon-related developmental regulator (IFRD)

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      50287732..50292429 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      50317089..50321785 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q12894.4 GenPept UniProtKB/Swiss-Prot:Q12894

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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