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    Iffo1 intermediate filament family orphan 1 [ Mus musculus (house mouse) ]

    Gene ID: 320678, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Iffo1provided by MGI
    Official Full Name
    intermediate filament family orphan 1provided by MGI
    Primary source
    MGI:MGI:2444516
    See related
    Ensembl:ENSMUSG00000038271 AllianceGenome:MGI:2444516
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Iffo; HOM-TES-103; 4733401N06Rik; A930037G23Rik
    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. Is expressed in diaphragm; embryo mesenchyme; and musculature. Orthologous to human IFFO1 (intermediate filament family orphan 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in adrenal adult (RPKM 25.6), spleen adult (RPKM 19.4) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    6 F2; 6 59.32 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (125122167..125138746)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (125145205..125161783)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene chromodomain helicase DNA binding protein 4 Neighboring gene predicted gene, 23751 Neighboring gene STARR-positive B cell enhancer ABC_E9675 Neighboring gene NOP2 nucleolar protein Neighboring gene STARR-seq mESC enhancer starr_17330 Neighboring gene STARR-positive B cell enhancer ABC_E2207 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: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Functional consequences of necdin nucleocytoplasmic localization. Lavi-Itzkovitz A, et al. PLoS One, 2012. PMID 22442722, Free PMC Article
    2. A CRISPR-based screen for Hedgehog signaling provides insights into ciliary function and ciliopathies. Breslow DK, et al. Nat Genet, 2018 Mar. PMID 29459677, Free PMC Article
    3. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Watahiki A, et al. Nat Methods, 2004 Dec. PMID 15782199
    4. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Hein MY, et al. Cell, 2015 Oct 22. PMID 26496610
    5. Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. Hansen GM, et al. Genome Res, 2008 Oct. PMID 18799693, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    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 membrane 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 nucleus IEA
    Inferred from Electronic Annotation
    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
    Names
    NHEJ 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_001039669.3 → NP_001034758.1  non-homologous end joining factor IFFO1 isoform a

      See identical proteins and their annotated locations for NP_001034758.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform a.
      Source sequence(s)
      AC166162, AK044728, AK163571, BY729723
      Consensus CDS
      CCDS39634.1
      UniProtKB/Swiss-Prot
      Q3TQI1, Q6PFE6, Q8BXL9, Q8BXS3, Q8C1D6
      Related
      ENSMUSP00000113088.3, ENSMUST00000117675.8
      Conserved Domains (1) summary
      pfam00038
      Location:230 → 521
      Filament; Intermediate filament protein

    2. NM_001302778.1 → NP_001289707.1  non-homologous end joining factor IFFO1 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses two alternate splice sites in the coding region but maintains the reading frame compared to variant 1. It encodes isoform c, which is the same length as isoform a.
      Source sequence(s)
      AK044728, AK163571, BC057601, BY729723
      UniProtKB/Swiss-Prot
      Q8BXL9
      Conserved Domains (1) summary
      pfam00038
      Location:230 → 521
      Filament; Intermediate filament protein

    3. NM_001302779.1 → NP_001289708.1  non-homologous end joining factor IFFO1 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an in-frame exon and uses an alternate in-frame splice site in the coding region compared to variant 1. The encoded protein (isoform d) is shorter than isoform a.
      Source sequence(s)
      AC166162, AK028273, AK044728, AK163571, BC057601, BY729723
      UniProtKB/Swiss-Prot
      Q8BXL9
      Related
      ENSMUST00000141230.8
      Conserved Domains (1) summary
      pfam00038
      Location:230 → 519
      Filament; Intermediate filament protein

    4. NM_178787.6 → NP_848902.4  non-homologous end joining factor IFFO1 isoform b

      See identical proteins and their annotated locations for NP_848902.4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region compared to variant 1. It encodes isoform b, which is shorter than isoform a.
      Source sequence(s)
      AK163571, BY729723
      Consensus CDS
      CCDS39635.1
      UniProtKB/Swiss-Prot
      Q8BXL9
      Related
      ENSMUSP00000113376.3, ENSMUST00000119527.8
      Conserved Domains (1) summary
      pfam00038
      Location:230 → 518
      Filament; Intermediate filament protein

    RNA

    1. NR_126495.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks an alternate exon and uses an alternate splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC166162, AK044709, AK163571, BC057601, BY729723
      Related
      ENSMUST00000144364.8

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000072.7 Reference GRCm39 C57BL/6J

      Range
      125122167..125138746
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036166235.1 → XP_036022128.1  non-homologous end joining factor IFFO1 isoform X6

      Conserved Domains (1) summary
      pfam00038
      Location:230 → 518
      Filament; Intermediate filament protein

    2. XM_036166234.1 → XP_036022127.1  non-homologous end joining factor IFFO1 isoform X5

      Conserved Domains (1) summary
      pfam00038
      Location:230 → 519
      Filament; Intermediate filament protein

    3. XM_006506274.4 → XP_006506337.2  non-homologous end joining factor IFFO1 isoform X1

      See identical proteins and their annotated locations for XP_006506337.2

      Conserved Domains (1) summary
      pfam00038
      Location:230 → 522
      Filament; Intermediate filament protein

    4. XM_006506275.4 → XP_006506338.2  non-homologous end joining factor IFFO1 isoform X1

      See identical proteins and their annotated locations for XP_006506338.2

      Conserved Domains (1) summary
      pfam00038
      Location:230 → 522
      Filament; Intermediate filament protein

    5. XM_006506278.5 → XP_006506341.2  non-homologous end joining factor IFFO1 isoform X3

      See identical proteins and their annotated locations for XP_006506341.2

      Conserved Domains (1) summary
      pfam00038
      Location:230 → 522
      Filament; Intermediate filament protein

    6. XM_006506279.5 → XP_006506342.2  non-homologous end joining factor IFFO1 isoform X3

      See identical proteins and their annotated locations for XP_006506342.2

      Conserved Domains (1) summary
      pfam00038
      Location:230 → 522
      Filament; Intermediate filament protein

    7. XM_036166233.1 → XP_036022126.1  non-homologous end joining factor IFFO1 isoform X4

      Conserved Domains (1) summary
      pfam00038
      Location:230 → 521
      Filament; Intermediate filament protein

    8. XM_030255464.1 → XP_030111324.1  non-homologous end joining factor IFFO1 isoform X2

      Conserved Domains (1) summary
      pfam00038
      Location:230 → 520
      Filament; Intermediate filament protein

    9. XM_006506280.4 → XP_006506343.2  non-homologous end joining factor IFFO1 isoform X7

      Conserved Domains (1) summary
      pfam00038
      Location:230 → 426
      Filament; Intermediate filament protein

    10. XM_006506281.4 → XP_006506344.2  non-homologous end joining factor IFFO1 isoform X8

      Conserved Domains (1) summary
      pfam00038
      Location:230 → 425
      Filament; Intermediate filament protein

    RNA

    1. XR_004942968.1 RNA Sequence

    2. XR_004942969.1 RNA Sequence

    3. XR_004942970.1 RNA Sequence

    4. XR_004942971.1 RNA Sequence

    5. XR_004942974.1 RNA Sequence

    6. XR_004942973.1 RNA Sequence

    7. XR_004942972.1 RNA Sequence

    8. XR_377466.5 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BXL9.1 GenPept UniProtKB/Swiss-Prot:Q8BXL9

    Gene LinkOut

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