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    FXN frataxin [ Homo sapiens (human) ]

    Gene ID: 2395, updated on 5-Mar-2024

    Summary

    Official Symbol
    FXNprovided by HGNC
    Official Full Name
    frataxinprovided by HGNC
    Primary source
    HGNC:HGNC:3951
    See related
    Ensembl:ENSG00000165060 MIM:606829; AllianceGenome:HGNC:3951
    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
    FA; X25; CyaY; FARR; FRDA
    Summary
    This nuclear gene encodes a mitochondrial protein which belongs to the FRATAXIN family. The protein functions in regulating mitochondrial iron transport and respiration. The expansion of intronic trinucleotide repeat GAA from 8-33 repeats to >90 repeats results in Friedreich ataxia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]
    Expression
    Ubiquitous expression in liver (RPKM 1.7), adrenal (RPKM 1.7) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See FXN in Genome Data Viewer
    Location:
    9q21.11
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (69035752..69079076)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (81209298..81252406)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (71650668..71693992)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol-4-phosphate 5-kinase type 1 beta Neighboring gene uncharacterized LOC101927069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28443 Neighboring gene Sharpr-MPRA regulatory region 10428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28444 Neighboring gene CRISPRi-validated cis-regulatory element chr9.764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28445 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19931 Neighboring gene Sharpr-MPRA regulatory region 187 Neighboring gene Friedreich ataxia repeat instability region Neighboring gene Sharpr-MPRA regulatory region 4997 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:71660286-71661281 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71669749-71670250 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71670251-71670750 Neighboring gene protein kinase cAMP-activated catalytic subunit gamma Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:71681521-71682120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:71683371-71683870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:71703383-71703883 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:71705161-71706130 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71731558-71732058 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71732059-71732559 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:71735458-71736416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19932 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:71745576-71746105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28446 Neighboring gene uncharacterized LOC124902175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28447 Neighboring gene tight junction protein 2 Neighboring gene Sharpr-MPRA regulatory region 4978 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71856696-71857196 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:71857197-71857697 Neighboring gene uncharacterized LOC124902176 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:71897736-71898504 Neighboring gene NANOG hESC enhancer GRCh37_chr9:71898508-71899009 Neighboring gene BRAF-activated non-protein coding RNA

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC57199

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 2 iron, 2 sulfur cluster binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables 2 iron, 2 sulfur cluster binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ferric iron binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ferric iron binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ferrous iron binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ferrous iron binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ferroxidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ferroxidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables iron chaperone activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables iron chaperone activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in [2Fe-2S] cluster assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of [4Fe-4S] cluster assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in [4Fe-4S] cluster assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in adult walking behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to hydrogen peroxide IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in embryo development ending in birth or egg hatching IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in heme biosynthetic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in intracellular iron ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in intracellular iron ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in iron incorporation into metallo-sulfur cluster IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in iron incorporation into metallo-sulfur cluster IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in iron ion transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in iron-sulfur cluster assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in iron-sulfur cluster assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in mitochondrion organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in muscle cell cellular homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of multicellular organism growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of organ growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of release of cytochrome c from mitochondria IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in organ growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in oxidative phosphorylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of aconitate hydratase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of catalytic activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of lyase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of lyase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of succinate dehydrogenase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in proprioception IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein autoprocessing IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of ferrochelatase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to iron ion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of L-cysteine desulfurase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of iron-sulfur cluster assembly complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of mitochondrial iron-sulfur cluster assembly complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrial matrix ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in mitochondrial matrix NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
     
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrion NAS
    Non-traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    frataxin, mitochondrial
    Names
    Friedreich ataxia protein
    NP_000135.2
    NP_852090.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_008845.2 RefSeqGene

      Range
      5190..48514
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_339

    mRNA and Protein(s)

    1. NM_000144.5NP_000135.2  frataxin, mitochondrial isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_000135.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AL162730, BC023633, U43747
      Consensus CDS
      CCDS6626.1
      UniProtKB/Swiss-Prot
      A8MXJ6, C9JJ89, O15545, O95656, Q15294, Q16595, Q5VZ01
      UniProtKB/TrEMBL
      A0A0S2Z3G4
      Related
      ENSP00000419243.2, ENST00000484259.3
      Conserved Domains (1) summary
      TIGR03422
      Location:94192
      mito_frataxin; frataxin
    2. NM_181425.3NP_852090.1  frataxin, mitochondrial isoform 2 preproprotein

      See identical proteins and their annotated locations for NP_852090.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, compared to variant 1, that results in a frameshift. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AA232366, AL162730, BC023633, BF058880
      Consensus CDS
      CCDS43834.1
      UniProtKB/TrEMBL
      A0A2R8Y5A1
      Related
      ENSP00000379652.2, ENST00000396366.6
      Conserved Domains (1) summary
      cl00238
      Location:94162
      Frataxin; Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      69035752..69079076
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      81209298..81252406
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001161706.1: Suppressed sequence

      Description
      NM_001161706.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.