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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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See Iffo1 in Genome Data Viewer
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

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