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    SLC41A3 solute carrier family 41 member 3 [ Homo sapiens (human) ]

    Gene ID: 54946, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SLC41A3provided by HGNC
    Official Full Name
    solute carrier family 41 member 3provided by HGNC
    Primary source
    HGNC:HGNC:31046
    See related
    Ensembl:ENSG00000114544 MIM:610803; AllianceGenome:HGNC:31046
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SLC41A1-L2
    Summary
    Enables magnesium:sodium antiporter activity. Involved in mitochondrial magnesium ion transmembrane transport. Located in mitochondrial inner membrane and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 23.3), ovary (RPKM 19.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC41A3 in Genome Data Viewer
    Location:
    3q21.2-q21.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (126006357..126101520, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (128738761..128834029, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (125725200..125820363, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ALG1 like 1, pseudogene Neighboring gene FBRSL1 pseudogene 1 Neighboring gene rhophilin associated tail protein 1B Neighboring gene ReSE screen-validated silencer GRCh37_chr3:125736296-125736478 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:125740258-125741040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125744116-125744616 Neighboring gene uncharacterized LOC124909425 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125777675-125778174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14672 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14673 Neighboring gene ALDH1L1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125822083-125822904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125831607-125832121 Neighboring gene aldehyde dehydrogenase 1 family member L1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125847779-125848549 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125850681-125851498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125855703-125856203 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125876969-125877469 Neighboring gene uncharacterized LOC105374083 Neighboring gene RNA, U1 small nuclear 30, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125899089-125899844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:125899845-125900598 Neighboring gene ALDH1L1 antisense RNA 2 Neighboring gene Sharpr-MPRA regulatory region 2719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20437 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:125926972-125928171

    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. SLC41A3 Exhibits as a Carcinoma Biomarker and Promoter in Liver Hepatocellular Carcinoma. Chang Q, et al. Comput Math Methods Med, 2021. PMID 34819993, Free PMC Article
    2. Solute carrier 41A3 encodes for a mitochondrial Mg(2+) efflux system. Mastrototaro L, et al. Sci Rep, 2016 Jun 15. PMID 27302215, Free PMC Article
    3. The human solute carrier SLC41A1 belongs to a novel eukaryotic subfamily with homology to prokaryotic MgtE Mg2+ transporters. Wabakken T, et al. Biochem Biophys Res Commun, 2003 Jul 4. PMID 12810078
    4. Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation. Virok DP, et al. J Proteome Res, 2011 Apr 1. PMID 21244100
    5. FAM105A/OTULINL Is a Pseudodeubiquitinase of the OTU-Class that Localizes to the ER Membrane. Ceccarelli DF, et al. Structure, 2019 Jun 4. PMID 31056421, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    • FLJ20473

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables magnesium:sodium antiporter 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 mitochondrial magnesium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in sodium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    solute carrier family 41 member 3
    Names
    SLC41A1-like 2

    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_001008485.2 → NP_001008485.2  solute carrier family 41 member 3 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC079848, AC092903, AC117422
      Consensus CDS
      CCDS33843.1
      UniProtKB/Swiss-Prot
      A6ND60, B3KSD9, B7Z4Y2, C9JE96, E7ENY4, Q8N342, Q8NB27, Q96GZ6, Q9H9I6, Q9HAB1, Q9NX30
      Related
      ENSP00000326070.6, ENST00000315891.10
      Conserved Domains (1) summary
      pfam01769
      Location:319 → 456
      MgtE; Divalent cation transporter

    2. NM_001008486.2 → NP_001008486.2  solute carrier family 41 member 3 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame coding exon and uses alternate splicing in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 3) with a unique C-terminus.
      Source sequence(s)
      AC079848, AC092903, AC117422
      Consensus CDS
      CCDS33842.1
      Related
      ENSP00000264471.6, ENST00000346785.9
      Conserved Domains (1) summary
      pfam01769
      Location:283 → 420
      MgtE; Divalent cation transporter

    3. NM_001008487.2 → NP_001008487.1  solute carrier family 41 member 3 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) utilizes an alternate 5' coding exon, compared to variant 1, resulting in the shortest protein (isoform 4) that has a unique N-terminus compared to isoform 1.
      Source sequence(s)
      AC092903, AC117422
      Consensus CDS
      CCDS33844.1
      UniProtKB/Swiss-Prot
      Q96GZ6
      Related
      ENSP00000373092.2, ENST00000383598.6
      Conserved Domains (1) summary
      pfam01769
      Location:80 → 211
      MgtE; Divalent cation transporter

    4. NM_001164475.2 → NP_001157947.1  solute carrier family 41 member 3 isoform 5

      See identical proteins and their annotated locations for NP_001157947.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' and 3' UTRs and coding sequences compared to variant 1. The resulting isoform (5) is shorter at the N-terminus and has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC079848, AC092903, AC117422
      Consensus CDS
      CCDS54635.1
      UniProtKB/Swiss-Prot
      Q96GZ6
      Related
      ENSP00000427409.1, ENST00000508835.5
      Conserved Domains (1) summary
      pfam01769
      Location:1 → 121
      MgtE; Divalent cation transporter

    5. NM_017836.4 → NP_060306.4  solute carrier family 41 member 3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses alternate splicing in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 2) with a unique C-terminus.
      Source sequence(s)
      AC079848, AC092903, AC117422
      Consensus CDS
      CCDS43144.1
      Related
      ENSP00000353533.4, ENST00000360370.9
      Conserved Domains (1) summary
      pfam01769
      Location:106 → 238
      MgtE; Divalent cation transporter

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      126006357..126101520 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005247563.3 → XP_005247620.1  solute carrier family 41 member 3 isoform X2

      See identical proteins and their annotated locations for XP_005247620.1

      UniProtKB/Swiss-Prot
      A6ND60, B3KSD9, B7Z4Y2, C9JE96, E7ENY4, Q8N342, Q8NB27, Q96GZ6, Q9H9I6, Q9HAB1, Q9NX30
      Conserved Domains (1) summary
      pfam01769
      Location:319 → 456
      MgtE; Divalent cation transporter

    2. XM_017006707.2 → XP_016862196.1  solute carrier family 41 member 3 isoform X5

      UniProtKB/Swiss-Prot
      Q96GZ6
      Conserved Domains (1) summary
      pfam01769
      Location:106 → 238
      MgtE; Divalent cation transporter

    3. XM_047448404.1 → XP_047304360.1  solute carrier family 41 member 3 isoform X1

    4. XM_017006708.1 → XP_016862197.1  solute carrier family 41 member 3 isoform X9

    5. XM_005247559.1 → XP_005247616.1  solute carrier family 41 member 3 isoform X1

      See identical proteins and their annotated locations for XP_005247616.1

      Conserved Domains (1) summary
      pfam01769
      Location:334 → 471
      MgtE; Divalent cation transporter

    6. XM_005247564.1 → XP_005247621.1  solute carrier family 41 member 3 isoform X3

      Conserved Domains (1) summary
      pfam01769
      Location:106 → 252
      MgtE; Divalent cation transporter

    7. XM_047448409.1 → XP_047304365.1  solute carrier family 41 member 3 isoform X9

    8. XM_006713681.4 → XP_006713744.1  solute carrier family 41 member 3 isoform X2

      See identical proteins and their annotated locations for XP_006713744.1

      UniProtKB/Swiss-Prot
      A6ND60, B3KSD9, B7Z4Y2, C9JE96, E7ENY4, Q8N342, Q8NB27, Q96GZ6, Q9H9I6, Q9HAB1, Q9NX30
      Conserved Domains (1) summary
      pfam01769
      Location:319 → 456
      MgtE; Divalent cation transporter

    9. XM_024453609.2 → XP_024309377.1  solute carrier family 41 member 3 isoform X5

      Conserved Domains (1) summary
      pfam01769
      Location:106 → 238
      MgtE; Divalent cation transporter

    10. XM_047448405.1 → XP_047304361.1  solute carrier family 41 member 3 isoform X1

    11. XM_047448406.1 → XP_047304362.1  solute carrier family 41 member 3 isoform X3

    12. XM_017006706.2 → XP_016862195.1  solute carrier family 41 member 3 isoform X5

      UniProtKB/Swiss-Prot
      Q96GZ6
      Conserved Domains (1) summary
      pfam01769
      Location:106 → 238
      MgtE; Divalent cation transporter

    13. XM_005247562.1 → XP_005247619.1  solute carrier family 41 member 3 isoform X2

      See identical proteins and their annotated locations for XP_005247619.1

      UniProtKB/Swiss-Prot
      A6ND60, B3KSD9, B7Z4Y2, C9JE96, E7ENY4, Q8N342, Q8NB27, Q96GZ6, Q9H9I6, Q9HAB1, Q9NX30
      Conserved Domains (1) summary
      pfam01769
      Location:319 → 456
      MgtE; Divalent cation transporter

    14. XM_024453610.1 → XP_024309378.1  solute carrier family 41 member 3 isoform X8

      Conserved Domains (1) summary
      pfam01769
      Location:283 → 420
      MgtE; Divalent cation transporter

    15. XM_017006709.1 → XP_016862198.1  solute carrier family 41 member 3 isoform X9

    16. XM_047448407.1 → XP_047304363.1  solute carrier family 41 member 3 isoform X3

    17. XM_017006705.2 → XP_016862194.1  solute carrier family 41 member 3 isoform X1

      Conserved Domains (1) summary
      pfam01769
      Location:334 → 471
      MgtE; Divalent cation transporter

    18. XM_047448411.1 → XP_047304367.1  solute carrier family 41 member 3 isoform X10

    19. XM_047448412.1 → XP_047304368.1  solute carrier family 41 member 3 isoform X11

    20. XM_005247565.3 → XP_005247622.1  solute carrier family 41 member 3 isoform X6

      Conserved Domains (1) summary
      pfam01769
      Location:293 → 430
      MgtE; Divalent cation transporter

    21. XM_011512945.2 → XP_011511247.1  solute carrier family 41 member 3 isoform X4

      Conserved Domains (1) summary
      pfam01769
      Location:308 → 445
      MgtE; Divalent cation transporter

    22. XM_047448408.1 → XP_047304364.1  solute carrier family 41 member 3 isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      128738761..128834029 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347017.1 → XP_054202992.1  solute carrier family 41 member 3 isoform X5

    2. XM_054347011.1 → XP_054202986.1  solute carrier family 41 member 3 isoform X2

    3. XM_054347007.1 → XP_054202982.1  solute carrier family 41 member 3 isoform X1

    4. XM_054347021.1 → XP_054202996.1  solute carrier family 41 member 3 isoform X9

    5. XM_054347006.1 → XP_054202981.1  solute carrier family 41 member 3 isoform X1

    6. XM_054347012.1 → XP_054202987.1  solute carrier family 41 member 3 isoform X3

    7. XM_054347016.1 → XP_054202991.1  solute carrier family 41 member 3 isoform X5

    8. XM_054347009.1 → XP_054202984.1  solute carrier family 41 member 3 isoform X2

    9. XM_054347013.1 → XP_054202988.1  solute carrier family 41 member 3 isoform X3

    10. XM_054347022.1 → XP_054202997.1  solute carrier family 41 member 3 isoform X9

    11. XM_054347010.1 → XP_054202985.1  solute carrier family 41 member 3 isoform X2

    12. XM_054347020.1 → XP_054202995.1  solute carrier family 41 member 3 isoform X8

    13. XM_054347023.1 → XP_054202998.1  solute carrier family 41 member 3 isoform X9

    14. XM_054347014.1 → XP_054202989.1  solute carrier family 41 member 3 isoform X3

    15. XM_054347008.1 → XP_054202983.1  solute carrier family 41 member 3 isoform X1

    16. XM_054347024.1 → XP_054202999.1  solute carrier family 41 member 3 isoform X10

    17. XM_054347025.1 → XP_054203000.1  solute carrier family 41 member 3 isoform X11

    18. XM_054347018.1 → XP_054202993.1  solute carrier family 41 member 3 isoform X6

    19. XM_054347015.1 → XP_054202990.1  solute carrier family 41 member 3 isoform X4

    20. XM_054347019.1 → XP_054202994.1  solute carrier family 41 member 3 isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96GZ6.2 GenPept UniProtKB/Swiss-Prot:Q96GZ6

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