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    AFG3L1P AFG3 like matrix AAA peptidase subunit 1, pseudogene [ Homo sapiens (human) ]

    Gene ID: 172, updated on 2-Nov-2024

    Summary

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    Official Symbol
    AFG3L1Pprovided by HGNC
    Official Full Name
    AFG3 like matrix AAA peptidase subunit 1, pseudogeneprovided by HGNC
    Primary source
    HGNC:HGNC:314
    See related
    Ensembl:ENSG00000293510 MIM:603020; AllianceGenome:HGNC:314
    Gene type
    pseudo
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    AFG3; AFG3L1
    Summary
    Predicted to be involved in protein processing. Predicted to act upstream of or within cristae formation; mitochondrial fusion; and mitochondrial protein processing. Predicted to be located in mitochondrial inner membrane. Predicted to be part of m-AAA complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in skin (RPKM 5.2), lymph node (RPKM 5.0) and 25 other tissues See more
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    Genomic context

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    See AFG3L1P in Genome Data Viewer
    Location:
    16q24.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (89972580..90000787)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (96058822..96087077)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (90038988..90067195)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11430 Neighboring gene small nucleolar RNA, H/ACA box 119 Neighboring gene differentially expressed in FDCP 8 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11431 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:90039036-90040019 Neighboring gene CENPB DNA-binding domain containing 1, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr16:90054784-90054958 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:90059900-90060881 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:90061681-90062880 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46884 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46891 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:90066749-90066899 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46902 Neighboring gene dysbindin domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7936 Neighboring gene Sharpr-MPRA regulatory region 21 Neighboring gene growth arrest specific 8 Neighboring gene GAS8 antisense RNA 1

    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. Variable and tissue-specific subunit composition of mitochondrial m-AAA protease complexes linked to hereditary spastic paraplegia. Koppen M, et al. Mol Cell Biol, 2007 Jan. PMID 17101804, Free PMC Article
    2. Chromosomal locations of three human nuclear genes (RPSM12, TUFM, and AFG3L1) specifying putative components of the mitochondrial gene expression apparatus. Shah ZH, et al. Genomics, 1998 Mar 15. PMID 9545647
    3. Genome-wide association study identifies three loci associated with melanoma risk. Bishop DT, et al. Nat Genet, 2009 Aug. PMID 19578364, Free PMC Article
    4. Molecular and functional analyses of the human and mouse genes encoding AFG3L1, a mitochondrial metalloprotease homologous to the human spastic paraplegia protein. Kremmidiotis G, et al. Genomics, 2001 Aug. PMID 11549317
    5. The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle. Warnatz HJ, et al. J Biol Chem, 2011 Jul 1. PMID 21555518, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. AFG3L1 is a functional target gene of the BACH1 transcription factor according to ChIP-seq and knockdown analysis in HEK 293 cells.
      Title: The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle.
    2. AFG3L1 is a mitochondrial ATP-dependent zinc metalloprotease transcribed into four mRNA isoforms that apparently are not translated in humans.
      Title: Molecular and functional analyses of the human and mouse genes encoding AFG3L1, a mitochondrial metalloprotease homologous to the human spastic paraplegia protein.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three loci associated with melanoma risk.
    EBI GWAS Catalog

    Variation

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    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

    Other Names

    • AFG3 (ATPase family gene 3, yeast)-like 1
    • AFG3 ATPase family gene 3-like 1, pseudogene
    • AFG3 ATPase family member 3-like 1, pseudogene
    • AFG3 like AAA ATPase 1, pseudogene

    Clone Names

    • FLJ45200

    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.

    RNA

    1. NR_003226.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AC092143, AK091293, BM986843, DA707802
      Related
      ENST00000437774.5

    2. NR_003227.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an internal exon, compared to variant 1.
      Source sequence(s)
      AC092143, AK097044, BM986843, DA707802
      Related
      ENST00000457926.5

    3. NR_003228.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains alternate 3' exons, as compared to variant 1.
      Source sequence(s)
      AC092143, AF329691, DA707802, DB318727
      Related
      ENST00000388970.8

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      89972580..90000787
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      96058822..96087077
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001031805.1: Suppressed sequence

      Description
      NM_001031805.1: This RefSeq was permanently suppressed because it is now thought that this locus is translationally silent in human.

    2. NM_001132.2: Suppressed sequence

      Description
      NM_001132.2: This RefSeq was permanently suppressed because it is now thought that this locus is translationally silent in human.
    Nucleotide Protein
    Heading Accession and Version

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