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    SLC25A39 solute carrier family 25 member 39 [ Homo sapiens (human) ]

    Gene ID: 51629, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SLC25A39provided by HGNC
    Official Full Name
    solute carrier family 25 member 39provided by HGNC
    Primary source
    HGNC:HGNC:24279
    See related
    Ensembl:ENSG00000013306 MIM:610820; AllianceGenome:HGNC:24279
    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
    CGI69; CGI-69
    Summary
    This gene encodes a member of the SLC25 transporter or mitochondrial carrier family of proteins. Members of this family are encoded by the nuclear genome while their protein products are usually embedded in the inner mitochondrial membrane and exhibit wide-ranging substrate specificity. Although the encoded protein is currently considered an orphan transporter, this protein is related to other carriers known to transport amino acids. This protein may play a role in iron homeostasis. [provided by RefSeq, Mar 2016]
    Expression
    Ubiquitous expression in bone marrow (RPKM 112.9), kidney (RPKM 47.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC25A39 in Genome Data Viewer
    Location:
    17q21.31
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (44319628..44324823, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (45172706..45177911, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (42396996..42402191, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RUNDC3A antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8587 Neighboring gene RNA, U6 small nuclear 453, pseudogene Neighboring gene RUN domain containing 3A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8588 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8589 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12255 Neighboring gene uncharacterized LOC124904009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42403114-42403965 Neighboring gene CRISPRi-validated cis-regulatory element chr17.2878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42420716-42421641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12260 Neighboring gene Sharpr-MPRA regulatory region 15390 Neighboring gene granulin precursor

    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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    Related articles in PubMed

    1. Overexpression of the human 2-oxoglutarate carrier lowers mitochondrial membrane potential in HEK-293 cells: contrast with the unique cold-induced mitochondrial carrier CGI-69. Yu XX, et al. Biochem J, 2001 Jan 15. PMID 11139402, Free PMC Article
    2. SLC25A39 links mitochondrial GSH sensing with iron metabolism. Chen X, et al. Mol Cell, 2024 Feb 15. PMID 38364779
    3. Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis. Shi X, et al. Mol Cell, 2024 Feb 15. PMID 38157846,
    4. Autoregulatory control of mitochondrial glutathione homeostasis. Liu Y, et al. Science, 2023 Nov 17. PMID 37917749, Free PMC Article
    5. Combinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS. Shi X, et al. Nat Commun, 2022 May 5. PMID 35513392, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SLC25A39 links mitochondrial GSH sensing with iron metabolism.
      Title: SLC25A39 links mitochondrial GSH sensing with iron metabolism.
    2. Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis.
      Title: Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis.
    3. Autoregulatory control of mitochondrial glutathione homeostasis.
      Title: Autoregulatory control of mitochondrial glutathione homeostasis.
    4. SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells.
      Title: SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells.
    5. Germinal GLT8D1, GATAD2A and SLC25A39 mutations in a patient with a glomangiopericytal tumor and five different sarcomas over a 10-year period.
      Title: Germinal GLT8D1, GATAD2A and SLC25A39 mutations in a patient with a glomangiopericytal tumor and five different sarcomas over a 10-year period.
    6. Compares and contrasts all the known human SLC25A* genes and includes functional information.
      Title: The mitochondrial transporter family SLC25: identification, properties and physiopathology.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    8. Required for functional heme biosynthesis in erythroid cells. Possibly regulate ALAS2 through iron-sulfur cluster biogenesis.
      Title: Discovery of genes essential for heme biosynthesis through large-scale gene expression analysis.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ22407

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 2 iron, 2 sulfur cluster binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables glutathione transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cellular response to iron ion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in glutathione import into mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in glutathione import into mitochondrion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in heme biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in import into the mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in mitochondrial inner membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    mitochondrial glutathione transporter SLC25A39
    Names
    probable mitochondrial glutathione transporter SLC25A39

    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_001143780.3 → NP_001137252.1  mitochondrial glutathione transporter SLC25A39 isoform a

      See identical proteins and their annotated locations for NP_001137252.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AK289357, BC096819
      Consensus CDS
      CCDS45700.1
      UniProtKB/Swiss-Prot
      A8JZZ2, D3DX51, D3DX54, Q4V9M1, Q9BZJ4, Q9P182, Q9UF66, Q9Y379
      Related
      ENSP00000366299.4, ENST00000377095.10
      Conserved Domains (1) summary
      pfam00153
      Location:251 → 350
      Mito_carr; Mitochondrial carrier protein

    2. NM_001321240.2 → NP_001308169.1  mitochondrial glutathione transporter SLC25A39 isoform c

      Status: REVIEWED

      Source sequence(s)
      AK294085, BU678976
      Consensus CDS
      CCDS82138.1
      UniProtKB/TrEMBL
      B4DFG5
      Related
      ENSP00000444540.1, ENST00000537904.6
      Conserved Domains (2) summary
      PTZ00169
      Location:16 → 308
      PTZ00169; ADP/ATP transporter on adenylate translocase; Provisional
      pfam00153
      Location:9 → 129
      Mito_carr; Mitochondrial carrier protein

    3. NM_001321241.2 → NP_001308170.1  mitochondrial glutathione transporter SLC25A39 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC003043, BU678976, CB960224
      Conserved Domains (1) summary
      pfam00153
      Location:9 → 144
      Mito_carr; Mitochondrial carrier protein

    4. NM_001366726.1 → NP_001353655.1  mitochondrial glutathione transporter SLC25A39 isoform e

      Status: REVIEWED

      Source sequence(s)
      AC003043
      UniProtKB/TrEMBL
      K7EMW3
      Conserved Domains (1) summary
      pfam00153
      Location:150 → 249
      Mito_carr; Mitochondrial carrier protein

    5. NM_016016.4 → NP_057100.1  mitochondrial glutathione transporter SLC25A39 isoform b

      See identical proteins and their annotated locations for NP_057100.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region compared to variant 1. The encoded isoform (b) is shorter but has the same N- and C-termini compared to isoform a.
      Source sequence(s)
      BC001398, CB960224
      Consensus CDS
      CCDS11482.1
      UniProtKB/Swiss-Prot
      Q9BZJ4
      Related
      ENSP00000225308.8, ENST00000225308.12
      Conserved Domains (1) summary
      pfam00153
      Location:9 → 144
      Mito_carr; Mitochondrial carrier protein

    RNA

    1. NR_159401.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC003043

    2. NR_159402.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC003043

    3. NR_159403.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC003043

    4. NR_159404.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC003043

    5. NR_159405.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC003043

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      44319628..44324823 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011524880.4 → XP_011523182.1  mitochondrial glutathione transporter SLC25A39 isoform X1

      Conserved Domains (1) summary
      pfam00153
      Location:257 → 356
      Mito_carr; Mitochondrial carrier protein

    2. XM_047436237.1 → XP_047292193.1  mitochondrial glutathione transporter SLC25A39 isoform X8

      UniProtKB/TrEMBL
      B4DFG5

    3. XM_047436236.1 → XP_047292192.1  mitochondrial glutathione transporter SLC25A39 isoform X2

    4. XM_047436235.1 → XP_047292191.1  mitochondrial glutathione transporter SLC25A39 isoform X7

    5. XM_047436234.1 → XP_047292190.1  mitochondrial glutathione transporter SLC25A39 isoform X1

    6. XM_047436240.1 → XP_047292196.1  mitochondrial glutathione transporter SLC25A39 isoform X3

      Related
      ENSP00000466615.1, ENST00000588767.5

    7. XM_047436238.1 → XP_047292194.1  mitochondrial glutathione transporter SLC25A39 isoform X3

    8. XM_047436241.1 → XP_047292197.1  mitochondrial glutathione transporter SLC25A39 isoform X4

      Related
      ENSP00000466676.1, ENST00000586016.5

    9. XM_047436239.1 → XP_047292195.1  mitochondrial glutathione transporter SLC25A39 isoform X3

    10. XM_047436242.1 → XP_047292198.1  mitochondrial glutathione transporter SLC25A39 isoform X5

    11. XM_047436244.1 → XP_047292200.1  mitochondrial glutathione transporter SLC25A39 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      45172706..45177911 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054316407.1 → XP_054172382.1  mitochondrial glutathione transporter SLC25A39 isoform X2

    2. XM_054316406.1 → XP_054172381.1  mitochondrial glutathione transporter SLC25A39 isoform X1

    3. XM_054316408.1 → XP_054172383.1  mitochondrial glutathione transporter SLC25A39 isoform X3

    4. XM_054316410.1 → XP_054172385.1  mitochondrial glutathione transporter SLC25A39 isoform X4

    5. XM_054316409.1 → XP_054172384.1  mitochondrial glutathione transporter SLC25A39 isoform X3

    6. XM_054316412.1 → XP_054172387.1  mitochondrial glutathione transporter SLC25A39 isoform X6

    7. XM_054316411.1 → XP_054172386.1  mitochondrial glutathione transporter SLC25A39 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BZJ4.2 GenPept UniProtKB/Swiss-Prot:Q9BZJ4

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