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

Gene ID: 362437, updated on 3-Apr-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
Ensembl: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, Apr 2022]
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, ENSRNOT00000048379.3
    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

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

    UniProtKB/TrEMBL
    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

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

    UniProtKB/TrEMBL
    A0A8I6A1J1, A0A8I6ACM7
    Related
    ENSRNOP00000085110.1
    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

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