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

    Gene ID: 25900, updated on 2-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
    mouse all
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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 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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    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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    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

      See identical proteins and their annotated locations for NP_001034759.1

      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

      See identical proteins and their annotated locations for NP_001180386.1

      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

      See identical proteins and their annotated locations for NP_542768.2

      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

      See identical proteins and their annotated locations for XP_006719039.1

      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

      See identical proteins and their annotated locations for XP_006719038.1

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

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