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    Iffo1 intermediate filament family orphan 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362437, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Iffo1provided by RGD
    Official Full Name
    intermediate filament family orphan 1provided by RGD
    Primary source
    RGD:1308257
    See related
    EnsemblRapid:ENSRNOG00000018533 AllianceGenome:RGD:1308257
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1308257
    Summary
    Predicted to be involved in DNA double-strand break attachment to nuclear envelope; double-strand break repair via nonhomologous end joining; and protein localization to site of double-strand break. Predicted to be located in nuclear matrix; nucleoplasm; and site of double-strand break. Orthologous to human IFFO1 (intermediate filament family orphan 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 95.4), Brain (RPKM 81.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Iffo1 in Genome Data Viewer
    Location:
    4q42
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (159631309..159648531)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (157945075..157962302)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (157659115..157676335)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene chromodomain helicase DNA binding protein 4 Neighboring gene small Cajal body-specific RNA 11 Neighboring gene NOP2 nucleolar protein Neighboring gene glyceraldehyde-3-phosphate dehydrogenase Neighboring gene non-SMC condensin I complex, subunit D2 Neighboring gene small Cajal body-specific RNA 10

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in DNA double-strand break attachment to nuclear envelope ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair via nonhomologous end joining ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization to site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in intermediate filament IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear matrix ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    non-homologous end joining factor IFFO1

    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_001108647.1 → NP_001102117.1  non-homologous end joining factor IFFO1

      See identical proteins and their annotated locations for NP_001102117.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473964
      UniProtKB/TrEMBL
      A0A8I6ACM7, A6ILS2, D3ZQI9
      Related
      ENSRNOP00000041102.2, ENSRNOT00000048379.4
      Conserved Domains (1) summary
      pfam00038
      Location:232 → 521
      Filament; Intermediate filament protein

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      159631309..159648531
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063286357.1 → XP_063142427.1  non-homologous end joining factor IFFO1 isoform X6

    2. XM_063286356.1 → XP_063142426.1  non-homologous end joining factor IFFO1 isoform X5

      UniProtKB/TrEMBL
      A6ILS4

    3. XM_063286355.1 → XP_063142425.1  non-homologous end joining factor IFFO1 isoform X4

      UniProtKB/TrEMBL
      A6ILS4, A6ILS5

    4. XM_039107897.2 → XP_038963825.1  non-homologous end joining factor IFFO1 isoform X3

      UniProtKB/TrEMBL
      A0A8I6ACM7
      Conserved Domains (1) summary
      pfam00038
      Location:232 → 427
      Filament; Intermediate filament protein

    5. XM_063286358.1 → XP_063142428.1  non-homologous end joining factor IFFO1 isoform X7

      UniProtKB/TrEMBL
      A0A8I6ACM7
      Related
      ENSRNOP00000085110.2, ENSRNOT00000113959.2

    6. XM_006237375.4 → XP_006237437.1  non-homologous end joining factor IFFO1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A1J1, A0A8I6ACM7
      Related
      ENSRNOP00000090501.2, ENSRNOT00000104044.2
      Conserved Domains (1) summary
      pfam00038
      Location:232 → 521
      Filament; Intermediate filament protein

    7. XM_006237376.5 → XP_006237438.1  non-homologous end joining factor IFFO1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6ACM7
      Conserved Domains (1) summary
      pfam00038
      Location:232 → 520
      Filament; Intermediate filament protein

    RNA

    1. XR_010065680.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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

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