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IFFO1 intermediate filament family orphan 1 [ Homo sapiens (human) ]

Gene ID: 25900, updated on 27-Nov-2024

Summary

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Official Symbol
IFFO1provided by HGNC
Official Full Name
intermediate filament family orphan 1provided by HGNC
Primary source
HGNC:HGNC:24970
See related
Ensembl:ENSG00000010295 MIM:610495; AllianceGenome:HGNC:24970
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
IFFO; HOM-TES-103
Summary
This gene is a member of the intermediate filament family. Intermediate filaments are proteins which are primordial components of the cytoskeleton and nuclear envelope. The proteins encoded by the members of this gene family are evolutionarily and structurally related but have limited sequence homology, with the exception of the central rod domain. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
Expression
Ubiquitous expression in spleen (RPKM 12.7), lymph node (RPKM 8.2) and 24 other tissues See more
Orthologs
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Genomic context

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See IFFO1 in Genome Data Viewer
Location:
12p13.31
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (6538961..6556042, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (6549317..6566401, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (6648127..6665208, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene non-SMC condensin I complex subunit D2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6641915-6642688 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6642689-6643462 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6643463-6644236 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6645785-6646558 Neighboring gene GAPDH divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5866 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6658582-6659082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6659083-6659583 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6660263-6660762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6661035-6661552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6663184-6663684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6663685-6664185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4171 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:6677307-6677928 Neighboring gene NOP2 nucleolar protein Neighboring gene Sharpr-MPRA regulatory region 3501 Neighboring gene chromodomain helicase DNA binding protein 4 Neighboring gene small Cajal body-specific RNA 11

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. Molecular and cellular biology of intermediate filaments. Steinert PM, et al. Annu Rev Biochem, 1988. PMID 3052284
  2. Intermediate filament proteins. Quinlan R, et al. Protein Profile, 1995. PMID 8771189
  3. CircIFFO1 suppresses tumor growth and metastasis of cutaneous squamous cell carcinoma by targeting the miR-424-5p/NFIB axis. Yu H, et al. Arch Dermatol Res, 2023 Nov. PMID 37405427
  4. METTL3-mediated N6-methyladenosine modification and HDAC5/YY1 promote IFFO1 downregulation in tumor development and chemo-resistance. Zhang Y, et al. Cancer Lett, 2023 Jan 28. PMID 36257380
  5. The nucleoskeleton protein IFFO1 immobilizes broken DNA and suppresses chromosome translocation during tumorigenesis. Li W, et al. Nat Cell Biol, 2019 Oct. PMID 31548606

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CircIFFO1 suppresses tumor growth and metastasis of cutaneous squamous cell carcinoma by targeting the miR-424-5p/NFIB axis.
    Title: CircIFFO1 suppresses tumor growth and metastasis of cutaneous squamous cell carcinoma by targeting the miR-424-5p/NFIB axis.
  2. METTL3-mediated N6-methyladenosine modification and HDAC5/YY1 promote IFFO1 downregulation in tumor development and chemo-resistance.
    Title: METTL3-mediated N6-methyladenosine modification and HDAC5/YY1 promote IFFO1 downregulation in tumor development and chemo-resistance.
  3. The lamin A/C-IFFO1-constituted nucleoskeleton prevents chromosome translocation by immobilizing broken DNA ends during tumorigenesis.
    Title: The nucleoskeleton protein IFFO1 immobilizes broken DNA and suppresses chromosome translocation during tumorigenesis.
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)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20703, MGC117359, DKFZp586I2223

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA double-strand break attachment to nuclear envelope IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in double-strand break repair via nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein localization to site of double-strand break IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in intermediate filament IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear inner membrane IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear matrix IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in site of double-strand break IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
non-homologous end joining factor IFFO1
Names
NHEJ factor IFFO1
intermediate filament-like MGC:2625

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_001039670.3 → NP_001034759.1  non-homologous end joining factor IFFO1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the central coding region, compared to variant 2, resulting in an isoform (4) that is 1 aa longer than isoform 2.
    Source sequence(s)
    AC006064, AI969315, BC002857, BC063004, BC110387
    Consensus CDS
    CCDS41741.1
    UniProtKB/Swiss-Prot
    Q0D2I5
    UniProtKB/TrEMBL
    Q6P593
    Related
    ENSP00000349364.4, ENST00000356896.8
    Conserved Domains (1) summary
    pfam00038
    Location:230 → 522
    Filament; Intermediate filament protein

  2. NM_001193457.2 → NP_001180386.1  non-homologous end joining factor IFFO1 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses two alternate in-frame splice sites in the central coding region, compared to variant 2, resulting in an isoform (5) that is longer than isoform 2.
    Source sequence(s)
    AI423929, AK298905, AL080214, BC063004, DA744744, DA969856
    Consensus CDS
    CCDS73425.1
    UniProtKB/TrEMBL
    A0A087WZ16
    Related
    ENSP00000482285.1, ENST00000619571.5
    Conserved Domains (1) summary
    pfam00038
    Location:230 → 530
    Filament; Intermediate filament protein

  3. NM_001330324.2 → NP_001317253.1  non-homologous end joining factor IFFO1 isoform 7

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) lacks an alternate in-frame exon in the central coding region, compared to variant 2, resulting in an isoform (7) that is 3 aa shorter than isoform 2.
    Source sequence(s)
    AA251428, AC006064, AF124432, AL548672, BC001790, BM147696, DN997252
    Consensus CDS
    CCDS81655.1
    UniProtKB/Swiss-Prot
    Q0D2I5, Q24JT6, Q7L5J9, Q7Z5X4, Q9BQ46
    Related
    ENSP00000380052.2, ENST00000396840.6

  4. NM_001330325.2 → NP_001317254.1  non-homologous end joining factor IFFO1 isoform 8

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) uses an alternate in-frame splice site in the central coding region, compared to variant 2, resulting in an isoform (8) that is 1 aa shorter than isoform 2.
    Source sequence(s)
    AA251428, AC006064, AF124432, AL548672, BC001790, BE410988, BM147696
    Conserved Domains (1) summary
    pfam00038
    Location:230 → 520
    Filament; Intermediate filament protein

  5. NM_080730.5 → NP_542768.2  non-homologous end joining factor IFFO1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes isoform 2.
    Source sequence(s)
    AA251428, AC006064, AF124432, AL548672, BC001790, BM147696
    Consensus CDS
    CCDS8550.2
    UniProtKB/Swiss-Prot
    Q0D2I5
    Related
    ENSP00000337593.4, ENST00000336604.8
    Conserved Domains (1) summary
    pfam00038
    Location:230 → 521
    Filament; Intermediate filament protein

RNA

  1. NR_036467.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) includes an additional internal exon in the 5' region and uses an alternate splice site in the central region, compared to variant 2. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA251428, AC006064, BC001790
    Related
    ENST00000487279.6

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    6538961..6556042 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006718976.5 → XP_006719039.1  non-homologous end joining factor IFFO1 isoform X9

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

  2. XM_011520949.4 → XP_011519251.1  non-homologous end joining factor IFFO1 isoform X5

    Conserved Domains (1) summary
    pfam00038
    Location:537 → 607
    Filament; Intermediate filament protein

  3. XM_006718975.5 → XP_006719038.1  non-homologous end joining factor IFFO1 isoform X8

    UniProtKB/Swiss-Prot
    Q0D2I5
    Conserved Domains (1) summary
    pfam00038
    Location:230 → 521
    Filament; Intermediate filament protein

  4. XM_011520948.4 → XP_011519250.1  non-homologous end joining factor IFFO1 isoform X4

    Conserved Domains (1) summary
    pfam00038
    Location:539 → 609
    Filament; Intermediate filament protein

  5. XM_047428690.1 → XP_047284646.1  non-homologous end joining factor IFFO1 isoform X2

  6. XM_011520947.4 → XP_011519249.1  non-homologous end joining factor IFFO1 isoform X3

    Conserved Domains (1) summary
    pfam00038
    Location:540 → 610
    Filament; Intermediate filament protein

  7. XM_047428692.1 → XP_047284648.1  non-homologous end joining factor IFFO1 isoform X7

  8. XM_047428689.1 → XP_047284645.1  non-homologous end joining factor IFFO1 isoform X1

  9. XM_047428693.1 → XP_047284649.1  non-homologous end joining factor IFFO1 isoform X10

  10. XM_047428691.1 → XP_047284647.1  non-homologous end joining factor IFFO1 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    6549317..6566401 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371715.1 → XP_054227690.1  non-homologous end joining factor IFFO1 isoform X9

  2. XM_054371711.1 → XP_054227686.1  non-homologous end joining factor IFFO1 isoform X5

  3. XM_054371714.1 → XP_054227689.1  non-homologous end joining factor IFFO1 isoform X8

  4. XM_054371710.1 → XP_054227685.1  non-homologous end joining factor IFFO1 isoform X4

  5. XM_054371708.1 → XP_054227683.1  non-homologous end joining factor IFFO1 isoform X2

  6. XM_054371709.1 → XP_054227684.1  non-homologous end joining factor IFFO1 isoform X3

  7. XM_054371713.1 → XP_054227688.1  non-homologous end joining factor IFFO1 isoform X7

  8. XM_054371707.1 → XP_054227682.1  non-homologous end joining factor IFFO1 isoform X1

  9. XM_054371716.1 → XP_054227691.1  non-homologous end joining factor IFFO1 isoform X10

  10. XM_054371712.1 → XP_054227687.1  non-homologous end joining factor IFFO1 isoform X6

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001193459.1: Suppressed sequence

    Description
    NM_001193459.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.

  2. NM_015438.1: Suppressed sequence

    Description
    NM_015438.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  3. NM_080731.3: Suppressed sequence

    Description
    NM_080731.3: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q0D2I5.2 GenPept UniProtKB/Swiss-Prot:Q0D2I5

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