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    PGS1 phosphatidylglycerophosphate synthase 1 [ Homo sapiens (human) ]

    Gene ID: 9489, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PGS1provided by HGNC
    Official Full Name
    phosphatidylglycerophosphate synthase 1provided by HGNC
    Primary source
    HGNC:HGNC:30029
    See related
    Ensembl:ENSG00000087157 MIM:614942; AllianceGenome:HGNC:30029
    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
    Summary
    Predicted to enable CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity and calcium ion binding activity. Predicted to be involved in cardiolipin biosynthetic process and diacylglycerol metabolic process. Located in endoplasmic reticulum. Is active in mitochondrion. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 9.6), appendix (RPKM 8.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PGS1 in Genome Data Viewer
    Location:
    17q25.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (78378649..78424659)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (79272180..79318173)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (76374730..76420740)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:76352361-76352860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76352918-76353567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9063 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:76355514-76356162 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9066 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9067 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76359520-76360097 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76361253-76361828 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76361829-76362406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12892 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76367859-76368426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76368427-76368994 Neighboring gene SOCS3 divergent transcript Neighboring gene suppressor of cytokine signaling 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76374619-76375580 Neighboring gene RNA, 7SL, cytoplasmic 236, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12894 Neighboring gene small nucleolar RNA SNORA30/SNORA37 family Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76396609-76397114 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76406789-76407334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76407335-76407878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12895 Neighboring gene Sharpr-MPRA regulatory region 14012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76413655-76414163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76415673-76416357 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76418631-76419210 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:76422004-76422504 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:76422505-76423005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76433212-76433840 Neighboring gene dynein axonemal heavy chain 17 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:76446189-76446410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76446540-76447118 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76461956-76462618 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76463282-76463943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12900 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9069 Neighboring gene DNAH17 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:76489132-76490331 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76493472-76494020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76494021-76494569 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:76502868-76504067 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:76506209-76507408 Neighboring gene RAN binding protein 1 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. Isolation of a chinese hamster ovary (CHO) cDNA encoding phosphatidylglycerophosphate (PGP) synthase, expression of which corrects the mitochondrial abnormalities of a PGP synthase-defective mutant of CHO-K1 cells. Kawasaki K, et al. J Biol Chem, 1999 Jan 15. PMID 9880566
    2. Purification of phosphatidylglycerophosphate synthase from Chinese hamster ovary cells. Kawasaki K, et al. Biochem J, 2001 Feb 15. PMID 11171073, Free PMC Article
    3. Mieap forms membrane-less organelles involved in cardiolipin metabolism. Ikari N, et al. iScience, 2024 Feb 16. PMID 38322995, Free PMC Article
    4. Sequence identification of 2,375 human brain genes. Adams MD, et al. Nature, 1992 Feb 13. PMID 1538749
    5. Biological, clinical and population relevance of 95 loci for blood lipids. Teslovich TM, et al. Nature, 2010 Aug 5. PMID 20686565, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    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

    EBI GWAS Catalog

    Description
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    • MGC131960, DKFZp762M186

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables calcium ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in cardiolipin biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cardiolipin biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cardiolipin biosynthetic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in diacylglycerol metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in phosphatidylglycerol biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in mitochondrial inner membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial
    Names
    PGP synthase 1
    NP_077733.3
    XP_011523789.1
    XP_011523790.1
    XP_011523791.1
    XP_016880846.1
    XP_016880847.1
    XP_016880848.1
    XP_016880849.1
    XP_016880850.1
    XP_016880853.1
    XP_047293057.1
    XP_047293058.1
    XP_047293059.1
    XP_047293060.1
    XP_047293061.1
    XP_054173832.1
    XP_054173833.1
    XP_054173834.1
    XP_054173835.1
    XP_054173836.1
    XP_054173837.1
    XP_054173838.1
    XP_054173839.1
    XP_054173840.1
    XP_054173841.1
    XP_054173842.1
    XP_054173843.1
    XP_054173844.1

    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_024419.5 → NP_077733.3  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial precursor

      See identical proteins and their annotated locations for NP_077733.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the functional protein.
      Source sequence(s)
      AK316147, BC108732, BI024108, ES314549
      Consensus CDS
      CCDS42391.1
      UniProtKB/Swiss-Prot
      B7ZA32, Q32NB8, Q8IYK9, Q8TA85, Q96A75, Q9H7G9, Q9NPW7
      UniProtKB/TrEMBL
      B4DL81
      Related
      ENSP00000262764.5, ENST00000262764.11
      Conserved Domains (3) summary
      cd09135
      Location:96 → 269
      PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
      cd09137
      Location:349 → 508
      PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
      pfam13091
      Location:113 → 265
      PLDc_2; PLD-like domain

    RNA

    1. NR_110601.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate internal and 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC035662, BC108732, BI024108, DC367136, ES314549
      Related
      ENST00000589426.5

    2. NR_110602.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate internal and 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK297156, BC108732, BI024108, DC367136, ES314549

    3. NR_111989.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate internal exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK024529, AK225030, BC108732, BI024108, ES314549
      Related
      ENST00000589425.5

    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
      78378649..78424659
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017025357.2 → XP_016880846.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X1

      Conserved Domains (3) summary
      cd09135
      Location:186 → 359
      PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
      cd09137
      Location:439 → 598
      PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
      pfam13091
      Location:203 → 355
      PLDc_2; PLD-like domain

    2. XM_017025358.2 → XP_016880847.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X1

      Conserved Domains (3) summary
      cd09135
      Location:186 → 359
      PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
      cd09137
      Location:439 → 598
      PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
      pfam13091
      Location:203 → 355
      PLDc_2; PLD-like domain

    3. XM_011525487.3 → XP_011523789.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X1

      Conserved Domains (3) summary
      cd09135
      Location:186 → 359
      PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
      cd09137
      Location:439 → 598
      PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
      pfam13091
      Location:203 → 355
      PLDc_2; PLD-like domain

    4. XM_017025360.2 → XP_016880849.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X4

      Conserved Domains (3) summary
      cd09135
      Location:186 → 359
      PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
      cd09137
      Location:439 → 558
      PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
      pfam13091
      Location:203 → 355
      PLDc_2; PLD-like domain

    5. XM_011525488.3 → XP_011523790.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X4

      Conserved Domains (3) summary
      cd09135
      Location:186 → 359
      PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
      cd09137
      Location:439 → 558
      PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
      pfam13091
      Location:203 → 355
      PLDc_2; PLD-like domain

    6. XM_017025359.2 → XP_016880848.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X3

    7. XM_047437101.1 → XP_047293057.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X2

    8. XM_017025361.3 → XP_016880850.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X6

      UniProtKB/Swiss-Prot
      B7ZA32, Q32NB8, Q8IYK9, Q8TA85, Q96A75, Q9H7G9, Q9NPW7
      UniProtKB/TrEMBL
      B4DL81
      Conserved Domains (3) summary
      cd09135
      Location:96 → 269
      PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
      cd09137
      Location:349 → 508
      PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
      pfam13091
      Location:113 → 265
      PLDc_2; PLD-like domain

    9. XM_047437103.1 → XP_047293059.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X9

    10. XM_017025364.3 → XP_016880853.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X8

      UniProtKB/TrEMBL
      B4DL81
      Conserved Domains (3) summary
      cd09135
      Location:96 → 243
      PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
      cd09137
      Location:323 → 482
      PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
      COG1502
      Location:95 → 521
      Cls; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase or related enzyme [Lipid transport and metabolism]

    11. XM_047437104.1 → XP_047293060.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X10

    12. XM_011525489.3 → XP_011523791.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X5

      Conserved Domains (3) summary
      cd09135
      Location:186 → 359
      PLDc_PGS1_euk_1; Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases
      cd09137
      Location:439 → 558
      PLDc_PGS1_euk_2; Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases
      pfam13091
      Location:203 → 355
      PLDc_2; PLD-like domain

    13. XM_047437105.1 → XP_047293061.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X11

    14. XM_047437102.1 → XP_047293058.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X7

    RNA

    1. XR_007065546.1 RNA Sequence

    2. XR_007065547.1 RNA Sequence

    3. XR_001752683.2 RNA Sequence

    4. XR_934604.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      79272180..79318173
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317864.1 → XP_054173839.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X6

      UniProtKB/Swiss-Prot
      B7ZA32, Q32NB8, Q8IYK9, Q8TA85, Q96A75, Q9H7G9, Q9NPW7

    2. XM_054317867.1 → XP_054173842.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X9

    3. XM_054317866.1 → XP_054173841.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X8

    4. XM_054317868.1 → XP_054173843.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X10

    5. XM_054317869.1 → XP_054173844.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X11

    6. XM_054317857.1 → XP_054173832.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X1

    7. XM_054317858.1 → XP_054173833.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X1

    8. XM_054317861.1 → XP_054173836.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X4

    9. XM_054317862.1 → XP_054173837.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X4

    10. XM_054317860.1 → XP_054173835.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X3

    11. XM_054317859.1 → XP_054173834.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X2

    12. XM_054317863.1 → XP_054173838.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X5

    13. XM_054317865.1 → XP_054173840.1  CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial isoform X7

    RNA

    1. XR_008484967.1 RNA Sequence

    2. XR_008484969.1 RNA Sequence

    3. XR_008484966.1 RNA Sequence

    4. XR_008484968.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q32NB8.1 GenPept UniProtKB/Swiss-Prot:Q32NB8

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