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    SLC25A29 solute carrier family 25 member 29 [ Homo sapiens (human) ]

    Gene ID: 123096, updated on 3-Nov-2024

    Summary

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    Official Symbol
    SLC25A29provided by HGNC
    Official Full Name
    solute carrier family 25 member 29provided by HGNC
    Primary source
    HGNC:HGNC:20116
    See related
    Ensembl:ENSG00000197119 MIM:615064; AllianceGenome:HGNC:20116
    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
    CACL; ORNT3; C14orf69
    Summary
    This gene encodes a nuclear-encoded mitochondrial protein that is a member of the large family of solute carrier family 25 (SLC25) mitochondrial transporters. The members of this superfamily are involved in numerous metabolic pathways and cell functions. This gene product was previously reported to be a mitochondrial carnitine-acylcarnitine-like (CACL) translocase (PMID:128829710) or an ornithine transporter (designated ORNT3, PMID:19287344), however, a recent study characterized the main role of this protein as a mitochondrial transporter of basic amino acids, with a preference for arginine and lysine (PMID:24652292). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Apr 2014]
    Expression
    Broad expression in thyroid (RPKM 41.5), prostate (RPKM 9.2) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC25A29 in Genome Data Viewer
    Location:
    14q32.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (100278567..100306444, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (94512311..94539478, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (100757453..100772781, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:100680080-100680580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9029 Neighboring gene YY1 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100684247-100684748 Neighboring gene Sharpr-MPRA regulatory region 8458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100698662-100699162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100699163-100699663 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:100704543-100705395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6081 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6083 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:100711928-100712136 Neighboring gene YY1 transcription factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100744670-100745650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6085 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6084 Neighboring gene microRNA 6764 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9033 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:100771717-100772283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6087 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6088 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9035 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100779917-100780815 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100784285-100784831 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9037 Neighboring gene microRNA 345 Neighboring gene RNA, 7SL, cytoplasmic 523, pseudogene

    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. Elevated mitochondrial SLC25A29 in cancer modulates metabolic status by increasing mitochondria-derived nitric oxide. Zhang H, et al. Oncogene, 2018 May. PMID 29459713
    2. The human gene SLC25A29, of solute carrier family 25, encodes a mitochondrial transporter of basic amino acids. Porcelli V, et al. J Biol Chem, 2014 May 9. PMID 24652292, Free PMC Article
    3. A novel mitochondrial carnitine-acylcarnitine translocase induced by partial hepatectomy and fasting. Sekoguchi E, et al. J Biol Chem, 2003 Oct 3. PMID 12882971
    4. The human and mouse SLC25A29 mitochondrial transporters rescue the deficient ornithine metabolism in fibroblasts of patients with the hyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome. Camacho JA, et al. Pediatr Res, 2009 Jul. PMID 19287344
    5. The mitochondrial transporter family SLC25: identification, properties and physiopathology. Palmieri F. Mol Aspects Med, 2013 Apr-Jun. PMID 23266187

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Results provide evidence that aberrant elevated SLC25A29 in cancer functioned to transport more arginine into mitochondria, improved mitochondria-derived nitric oxide levels, thus modulated metabolic status to facilitate increased cancer progression.
      Title: Elevated mitochondrial SLC25A29 in cancer modulates metabolic status by increasing mitochondria-derived nitric oxide.
    2. The main physiological role of SLC25A29 is to import basic amino acids into mitochondria for mitochondrial protein synthesis and amino acid degradation.
      Title: The human gene SLC25A29, of solute carrier family 25, encodes a mitochondrial transporter of basic amino acids.
    3. Compares and contrasts all the known human SLC25A* genes and includes functional information.
      Title: The mitochondrial transporter family SLC25: identification, properties and physiopathology.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    5. The human and mouse SLC25A29 mitochondrial ornithine transporters (designated as ORNT3) rescue the deficient ornithine metabolism in fibroblasts of patients with the hyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome.
      Title: The human and mouse SLC25A29 mitochondrial transporters rescue the deficient ornithine metabolism in fibroblasts of patients with the hyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome.
    Submit: New GeneRIF Correction

    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)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ38975, AL157871.2

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables acyl carnitine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables basic amino acid transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables basic amino acid transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		  
    enables high-affinity L-arginine transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables high-affinity L-arginine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables high-affinity lysine transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables high-affinity lysine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in L-arginine transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in L-histidine transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in L-lysine transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT involved_in acyl carnitine transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in amino acid transport TAS
    Traceable Author Statement
    more info
    		  
    NOT involved_in carnitine transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mitochondrial L-ornithine transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrial L-ornithine transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ornithine transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    mitochondrial basic amino acids transporter
    Names
    carnitine-acylcarnitine translocase like
    mitochondrial carnitine/acylcarnitine carrier protein CACL
    mitochondrial ornithine transporter 3
    solute carrier family 25 (mitochondrial carnitine/acylcarnitine carrier), member 29

    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_001039355.3 → NP_001034444.1  mitochondrial basic amino acids transporter isoform 1

      See identical proteins and their annotated locations for NP_001034444.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      BX247983, CF529947
      Consensus CDS
      CCDS32156.1
      UniProtKB/Swiss-Prot
      A3KMR5, Q541V0, Q8N8R3
      Related
      ENSP00000352167.3, ENST00000359232.8
      Conserved Domains (2) summary
      PTZ00169
      Location:2 → 259
      PTZ00169; ADP/ATP transporter on adenylate translocase; Provisional
      pfam00153
      Location:185 → 268
      Mito_carr; Mitochondrial carrier protein

    2. NM_001291813.2 → NP_001278742.1  mitochondrial basic amino acids transporter isoform 2

      See identical proteins and their annotated locations for NP_001278742.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an additional exon that causes a frame-shift and results in the use of an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2-4 encode the same isoform.
      Source sequence(s)
      AK310069, BI828620, BX247983, CF529947
      UniProtKB/Swiss-Prot
      Q8N8R3
      Conserved Domains (1) summary
      pfam00153
      Location:123 → 202
      Mito_carr; Mitochondrial carrier protein

    3. NM_001291814.2 → NP_001278743.1  mitochondrial basic amino acids transporter isoform 2

      See identical proteins and their annotated locations for NP_001278743.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an additional exon that causes a frame-shift and results in the use of an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2-4 encode the same isoform.
      Source sequence(s)
      BX247983, CF529947, DA201175
      UniProtKB/Swiss-Prot
      Q8N8R3
      Conserved Domains (1) summary
      pfam00153
      Location:123 → 202
      Mito_carr; Mitochondrial carrier protein

    4. NM_001352820.2 → NP_001339749.1  mitochondrial basic amino acids transporter isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL157871
      Conserved Domains (1) summary
      pfam00153
      Location:123 → 202
      Mito_carr; Mitochondrial carrier protein

    5. NM_001352821.2 → NP_001339750.1  mitochondrial basic amino acids transporter isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL157871
      Conserved Domains (1) summary
      pfam00153
      Location:238 → 321
      Mito_carr; Mitochondrial carrier protein

    6. NM_001352822.2 → NP_001339751.1  mitochondrial basic amino acids transporter isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL157871
      Conserved Domains (1) summary
      pfam00153
      Location:123 → 202
      Mito_carr; Mitochondrial carrier protein

    7. NM_001352823.2 → NP_001339752.1  mitochondrial basic amino acids transporter isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL157871
      Conserved Domains (1) summary
      pfam00153
      Location:123 → 202
      Mito_carr; Mitochondrial carrier protein

    8. NM_152333.4 → NP_689546.1  mitochondrial basic amino acids transporter isoform 2

      See identical proteins and their annotated locations for NP_689546.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an internal exon that causes a frame-shift and results in the use of an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2-4 encode the same isoform.
      Source sequence(s)
      AK096294, BX247983, CF529947
      UniProtKB/Swiss-Prot
      Q8N8R3
      Related
      ENSP00000450913.1, ENST00000554912.1
      Conserved Domains (1) summary
      pfam00153
      Location:123 → 202
      Mito_carr; Mitochondrial carrier protein

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      100278567..100306444 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047430952.1 → XP_047286908.1  mitochondrial basic amino acids transporter isoform X5

    2. XM_006720039.5 → XP_006720102.1  mitochondrial basic amino acids transporter isoform X3

      Conserved Domains (1) summary
      pfam00153
      Location:224 → 307
      Mito_carr; Mitochondrial carrier protein

    3. XM_047430946.1 → XP_047286902.1  mitochondrial basic amino acids transporter isoform X1

    4. XM_047430949.1 → XP_047286905.1  mitochondrial basic amino acids transporter isoform X4

    5. XM_047430959.1 → XP_047286915.1  mitochondrial basic amino acids transporter isoform X5

    6. XM_047430948.1 → XP_047286904.1  mitochondrial basic amino acids transporter isoform X2

    7. XM_047430947.1 → XP_047286903.1  mitochondrial basic amino acids transporter isoform X2

    8. XM_047430951.1 → XP_047286907.1  mitochondrial basic amino acids transporter isoform X5

    9. XM_047430962.1 → XP_047286918.1  mitochondrial basic amino acids transporter isoform X5

    10. XM_047430956.1 → XP_047286912.1  mitochondrial basic amino acids transporter isoform X5

    11. XM_047430950.1 → XP_047286906.1  mitochondrial basic amino acids transporter isoform X5

    12. XM_047430961.1 → XP_047286917.1  mitochondrial basic amino acids transporter isoform X5

    13. XM_047430958.1 → XP_047286914.1  mitochondrial basic amino acids transporter isoform X5

      Related
      ENSP00000452446.1, ENST00000556505.5

    14. XM_047430954.1 → XP_047286910.1  mitochondrial basic amino acids transporter isoform X5

    15. XM_047430960.1 → XP_047286916.1  mitochondrial basic amino acids transporter isoform X5

    16. XM_047430957.1 → XP_047286913.1  mitochondrial basic amino acids transporter isoform X5

    17. XM_047430953.1 → XP_047286909.1  mitochondrial basic amino acids transporter isoform X5

    RNA

    1. XR_007063984.1 RNA Sequence

    2. XR_007063981.1 RNA Sequence

    3. XR_007063983.1 RNA Sequence

    4. XR_007063982.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      94512311..94539478 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375418.1 → XP_054231393.1  mitochondrial basic amino acids transporter isoform X5

    2. XM_054375413.1 → XP_054231388.1  mitochondrial basic amino acids transporter isoform X3

    3. XM_054375415.1 → XP_054231390.1  mitochondrial basic amino acids transporter isoform X5

    4. XM_054375410.1 → XP_054231385.1  mitochondrial basic amino acids transporter isoform X1

    5. XM_054375414.1 → XP_054231389.1  mitochondrial basic amino acids transporter isoform X4

    6. XM_054375424.1 → XP_054231399.1  mitochondrial basic amino acids transporter isoform X5

    7. XM_054375411.1 → XP_054231386.1  mitochondrial basic amino acids transporter isoform X2

    8. XM_054375417.1 → XP_054231392.1  mitochondrial basic amino acids transporter isoform X5

    9. XM_054375426.1 → XP_054231401.1  mitochondrial basic amino acids transporter isoform X5

    10. XM_054375423.1 → XP_054231398.1  mitochondrial basic amino acids transporter isoform X5

    11. XM_054375425.1 → XP_054231400.1  mitochondrial basic amino acids transporter isoform X5

    12. XM_054375422.1 → XP_054231397.1  mitochondrial basic amino acids transporter isoform X5

    13. XM_054375420.1 → XP_054231395.1  mitochondrial basic amino acids transporter isoform X5

    14. XM_054375419.1 → XP_054231394.1  mitochondrial basic amino acids transporter isoform X5

    15. XM_054375412.1 → XP_054231387.1  mitochondrial basic amino acids transporter isoform X2

    16. XM_054375427.1 → XP_054231402.1  mitochondrial basic amino acids transporter isoform X5

    17. XM_054375421.1 → XP_054231396.1  mitochondrial basic amino acids transporter isoform X5

    18. XM_054375416.1 → XP_054231391.1  mitochondrial basic amino acids transporter isoform X5

    RNA

    1. XR_008488822.1 RNA Sequence

    2. XR_008488819.1 RNA Sequence

    3. XR_008488821.1 RNA Sequence

    4. XR_008488820.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N8R3.2 GenPept UniProtKB/Swiss-Prot:Q8N8R3

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