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    ATP13A3 ATPase 13A3 [ Homo sapiens (human) ]

    Gene ID: 79572, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ATP13A3provided by HGNC
    Official Full Name
    ATPase 13A3provided by HGNC
    Primary source
    HGNC:HGNC:24113
    See related
    Ensembl:ENSG00000133657 MIM:610232; AllianceGenome:HGNC:24113
    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
    PPH5; AFURS1
    Summary
    ATP13A3 is a member of the P-type ATPase family of proteins that transport a variety of cations across membranes. Other P-type ATPases include ATP7B (MIM 606882) and ATP7A (MIM 300011).[supplied by OMIM, Aug 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 24.7), appendix (RPKM 18.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ATP13A3 in Genome Data Viewer
    Location:
    3q29
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (194402677..194494334, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (197101099..197192872, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (194123406..194207731, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194089931-194090895 Neighboring gene leucine rich repeat containing 15 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15021 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194120825-194121378 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194121379-194121931 Neighboring gene glycoprotein V platelet Neighboring gene MPRA-validated peak4979 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:194167532-194168731 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:194170227-194171426 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15023 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21025 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21026 Neighboring gene ATP13A3 divergent transcript Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:194218672-194219871 Neighboring gene Sharpr-MPRA regulatory region 12272 Neighboring gene Sharpr-MPRA regulatory regions 5224 and 9858 Neighboring gene RNA, U6 small nuclear 1101, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21027 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:194274365-194274563 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:194276967-194277466 Neighboring gene ribosomal protein L23a pseudogene 93

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Cloning the AFURS1 gene which is up-regulated in senescent human parenchymal kidney cells. Habtemichael N, et al. Gene, 2002 Jan 23. PMID 11867234
    2. Pairing a prognostic target with potential therapeutic strategy for head and neck cancer. Lek SM, et al. Oral Oncol, 2020 Dec. PMID 33091845
    3. ATP13A3 variants promote pulmonary arterial hypertension by disrupting polyamine transport. Liu B, et al. Cardiovasc Res, 2024 May 29. PMID 38626311, Free PMC Article
    4. ATP13A3 is a major component of the enigmatic mammalian polyamine transport system. Hamouda NN, et al. J Biol Chem, 2021 Jan-Jun. PMID 33310703, Free PMC Article
    5. A Combined Targeted and Whole Exome Sequencing Approach Identified Novel Candidate Genes Involved in Heritable Pulmonary Arterial Hypertension. Barozzi C, et al. Sci Rep, 2019 Jan 24. PMID 30679663, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ATP13A3 variants promote pulmonary arterial hypertension by disrupting polyamine transport.
      Title: ATP13A3 variants promote pulmonary arterial hypertension by disrupting polyamine transport.
    2. Pairing a prognostic target with potential therapeutic strategy for head and neck cancer.
      Title: Pairing a prognostic target with potential therapeutic strategy for head and neck cancer.
    3. In addition to EIF2AK4, which has been already suggested to be associated with pulmonary veno-occlusive disease, we identified the novel candidate genes ATP13A3, CD248, EFCAB4B, involved in lung vascular remodeling that represent reliable drivers contributing to the disease according to their biological functions/inheritance patterns
      Title: A Combined Targeted and Whole Exome Sequencing Approach Identified Novel Candidate Genes Involved in Heritable Pulmonary Arterial Hypertension.
    4. Case-control analyses reveal significant overrepresentation of rare variants in ATP13A3, AQP1 and SOX17, and provide independent validation of a critical role for GDF2 in heritable pulmonary arterial hypertension.
      Title: Identification of rare sequence variation underlying heritable pulmonary arterial hypertension.
    5. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    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

    Associated conditions

    Description Tests
    Pulmonary hypertension, primary, autosomal recessive
    MedGen: C5676877 OMIM: 265400 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of ATP13A3 PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ90613, DKFZp686K16189

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ABC-type putrescine transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATPase-coupled monoatomic cation transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables P-type ion transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables P-type transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables polyamine transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in intracellular calcium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in monoatomic cation transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in polyamine transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in putrescine transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in late endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane HDA PubMed 
    located_in recycling endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    polyamine-transporting ATPase 13A3
    Names
    ATPase family homolog up-regulated in senescence cells 1
    ATPase type 13A3
    probable cation-transporting ATPase 13A3
    putrescine transporting ATPase
    NP_001354478.1
    NP_001361765.1
    NP_078800.3
    XP_005269414.1
    XP_011511423.1
    XP_011511425.1
    XP_011511426.1
    XP_047304860.1
    XP_047304861.1
    XP_047304862.1
    XP_047304863.1
    XP_047304864.1
    XP_047304865.1
    XP_047304866.1
    XP_047304867.1
    XP_047304868.1
    XP_047304869.1
    XP_047304870.1
    XP_047304871.1
    XP_047304872.1
    XP_054203818.1
    XP_054203819.1
    XP_054203820.1
    XP_054203821.1
    XP_054203822.1
    XP_054203823.1
    XP_054203824.1
    XP_054203825.1
    XP_054203826.1
    XP_054203827.1
    XP_054203828.1
    XP_054203829.1
    XP_054203830.1
    XP_054203831.1
    XP_054203832.1

    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_001367549.1 → NP_001354478.1  polyamine-transporting ATPase 13A3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC108676, AC125362
      Consensus CDS
      CCDS93438.1
      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7
      Related
      ENSP00000494937.2, ENST00000645319.2

    2. NM_001374836.1 → NP_001361765.1  polyamine-transporting ATPase 13A3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC108676, AC125362
      UniProtKB/TrEMBL
      A0A2R8YDN7
      Conserved Domains (1) summary
      TIGR01657
      Location:14 → 1122
      P-ATPase-V; P-type ATPase of unknown pump specificity (type V)

    3. NM_024524.4 → NP_078800.3  polyamine-transporting ATPase 13A3 isoform 1

      See identical proteins and their annotated locations for NP_078800.3

      Status: VALIDATED

      Source sequence(s)
      AC108676, AK075094, AK225064, BC106085, BP313821, DA852339, DR005713, DV080200
      Consensus CDS
      CCDS43187.1
      UniProtKB/Swiss-Prot
      Q8NC11, Q96KS1, Q9H7F0
      UniProtKB/TrEMBL
      A0A2R8YDN7
      Related
      ENSP00000416508.1, ENST00000439040.6
      Conserved Domains (6) summary
      TIGR01657
      Location:14 → 1149
      P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
      pfam00122
      Location:236 → 483
      E1-E2_ATPase; E1-E2 ATPase
      pfam00690
      Location:178 → 226
      Cation_ATPase_N; Cation transporter/ATPase, N-terminus
      pfam12409
      Location:13 → 145
      P5-ATPase; P5-type ATPase cation transporter
      pfam13246
      Location:622 → 662
      Cation_ATPase; Cation transport ATPase (P-type)
      cl21460
      Location:821 → 898
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    RNA

    1. NR_164666.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC108676, AC125362

    2. NR_164667.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC108676, AC125362

    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
      194402677..194494334 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448912.1 → XP_047304868.1  polyamine-transporting ATPase 13A3 isoform X3

      UniProtKB/Swiss-Prot
      Q8NC11, Q96KS1, Q9H7F0
      UniProtKB/TrEMBL
      A0A2R8YDN7
      Related
      ENST00000687055.1

    2. XM_047448909.1 → XP_047304865.1  polyamine-transporting ATPase 13A3 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7

    3. XM_047448904.1 → XP_047304860.1  polyamine-transporting ATPase 13A3 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7

    4. XM_047448910.1 → XP_047304866.1  polyamine-transporting ATPase 13A3 isoform X2

      UniProtKB/TrEMBL
      A0A2R8YDN7
      Related
      ENST00000690810.1

    5. XM_047448913.1 → XP_047304869.1  polyamine-transporting ATPase 13A3 isoform X3

      UniProtKB/Swiss-Prot
      Q8NC11, Q96KS1, Q9H7F0
      UniProtKB/TrEMBL
      A0A2R8YDN7
      Related
      ENSP00000493923.2, ENST00000642744.2

    6. XM_047448916.1 → XP_047304872.1  polyamine-transporting ATPase 13A3 isoform X5

      UniProtKB/TrEMBL
      A0A2R8YDN7

    7. XM_011513123.3 → XP_011511425.1  polyamine-transporting ATPase 13A3 isoform X3

      See identical proteins and their annotated locations for XP_011511425.1

      UniProtKB/Swiss-Prot
      Q8NC11, Q96KS1, Q9H7F0
      UniProtKB/TrEMBL
      A0A2R8YDN7
      Related
      ENSP00000494471.1, ENST00000645538.1
      Conserved Domains (6) summary
      TIGR01657
      Location:14 → 1149
      P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
      pfam00122
      Location:236 → 483
      E1-E2_ATPase; E1-E2 ATPase
      pfam00690
      Location:178 → 226
      Cation_ATPase_N; Cation transporter/ATPase, N-terminus
      pfam12409
      Location:13 → 145
      P5-ATPase; P5-type ATPase cation transporter
      pfam13246
      Location:622 → 662
      Cation_ATPase; Cation transport ATPase (P-type)
      cl21460
      Location:821 → 898
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    8. XM_047448911.1 → XP_047304867.1  polyamine-transporting ATPase 13A3 isoform X2

      UniProtKB/TrEMBL
      A0A2R8YDN7

    9. XM_047448914.1 → XP_047304870.1  polyamine-transporting ATPase 13A3 isoform X3

      UniProtKB/Swiss-Prot
      Q8NC11, Q96KS1, Q9H7F0
      UniProtKB/TrEMBL
      A0A2R8YDN7

    10. XM_047448906.1 → XP_047304862.1  polyamine-transporting ATPase 13A3 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7

    11. XM_047448915.1 → XP_047304871.1  polyamine-transporting ATPase 13A3 isoform X3

      UniProtKB/Swiss-Prot
      Q8NC11, Q96KS1, Q9H7F0
      UniProtKB/TrEMBL
      A0A2R8YDN7

    12. XM_047448905.1 → XP_047304861.1  polyamine-transporting ATPase 13A3 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7

    13. XM_047448907.1 → XP_047304863.1  polyamine-transporting ATPase 13A3 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7

    14. XM_047448908.1 → XP_047304864.1  polyamine-transporting ATPase 13A3 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7

    15. XM_005269357.4 → XP_005269414.1  polyamine-transporting ATPase 13A3 isoform X1

      See identical proteins and their annotated locations for XP_005269414.1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7
      Conserved Domains (6) summary
      TIGR01657
      Location:14 → 1149
      P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
      pfam00122
      Location:236 → 483
      E1-E2_ATPase; E1-E2 ATPase
      pfam00690
      Location:178 → 226
      Cation_ATPase_N; Cation transporter/ATPase, N-terminus
      pfam12409
      Location:13 → 145
      P5-ATPase; P5-type ATPase cation transporter
      pfam13246
      Location:622 → 662
      Cation_ATPase; Cation transport ATPase (P-type)
      cl21460
      Location:821 → 898
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    16. XM_011513121.2 → XP_011511423.1  polyamine-transporting ATPase 13A3 isoform X1

      See identical proteins and their annotated locations for XP_011511423.1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7
      Conserved Domains (6) summary
      TIGR01657
      Location:14 → 1149
      P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
      pfam00122
      Location:236 → 483
      E1-E2_ATPase; E1-E2 ATPase
      pfam00690
      Location:178 → 226
      Cation_ATPase_N; Cation transporter/ATPase, N-terminus
      pfam12409
      Location:13 → 145
      P5-ATPase; P5-type ATPase cation transporter
      pfam13246
      Location:622 → 662
      Cation_ATPase; Cation transport ATPase (P-type)
      cl21460
      Location:821 → 898
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    17. XM_011513124.4 → XP_011511426.1  polyamine-transporting ATPase 13A3 isoform X4

      UniProtKB/TrEMBL
      A0A2R8YDN7
      Conserved Domains (6) summary
      TIGR01657
      Location:14 → 1149
      P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
      pfam00122
      Location:236 → 483
      E1-E2_ATPase; E1-E2 ATPase
      pfam00690
      Location:178 → 226
      Cation_ATPase_N; Cation transporter/ATPase, N-terminus
      pfam12409
      Location:13 → 145
      P5-ATPase; P5-type ATPase cation transporter
      pfam13246
      Location:622 → 662
      Cation_ATPase; Cation transport ATPase (P-type)
      cl21460
      Location:821 → 898
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      197101099..197192872 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347852.1 → XP_054203827.1  polyamine-transporting ATPase 13A3 isoform X3

      UniProtKB/Swiss-Prot
      Q8NC11, Q96KS1, Q9H7F0
      UniProtKB/TrEMBL
      A0A2R8YDN7

    2. XM_054347843.1 → XP_054203818.1  polyamine-transporting ATPase 13A3 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7

    3. XM_054347849.1 → XP_054203824.1  polyamine-transporting ATPase 13A3 isoform X2

      UniProtKB/TrEMBL
      A0A2R8YDN7

    4. XM_054347853.1 → XP_054203828.1  polyamine-transporting ATPase 13A3 isoform X3

      UniProtKB/Swiss-Prot
      Q8NC11, Q96KS1, Q9H7F0
      UniProtKB/TrEMBL
      A0A2R8YDN7

    5. XM_054347857.1 → XP_054203832.1  polyamine-transporting ATPase 13A3 isoform X5

      UniProtKB/TrEMBL
      A0A2R8YDN7

    6. XM_054347851.1 → XP_054203826.1  polyamine-transporting ATPase 13A3 isoform X3

      UniProtKB/Swiss-Prot
      Q8NC11, Q96KS1, Q9H7F0
      UniProtKB/TrEMBL
      A0A2R8YDN7

    7. XM_054347850.1 → XP_054203825.1  polyamine-transporting ATPase 13A3 isoform X2

      UniProtKB/TrEMBL
      A0A2R8YDN7

    8. XM_054347854.1 → XP_054203829.1  polyamine-transporting ATPase 13A3 isoform X3

      UniProtKB/Swiss-Prot
      Q8NC11, Q96KS1, Q9H7F0
      UniProtKB/TrEMBL
      A0A2R8YDN7

    9. XM_054347845.1 → XP_054203820.1  polyamine-transporting ATPase 13A3 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7

    10. XM_054347855.1 → XP_054203830.1  polyamine-transporting ATPase 13A3 isoform X3

      UniProtKB/Swiss-Prot
      Q8NC11, Q96KS1, Q9H7F0
      UniProtKB/TrEMBL
      A0A2R8YDN7

    11. XM_054347844.1 → XP_054203819.1  polyamine-transporting ATPase 13A3 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7

    12. XM_054347846.1 → XP_054203821.1  polyamine-transporting ATPase 13A3 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7

    13. XM_054347847.1 → XP_054203822.1  polyamine-transporting ATPase 13A3 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7

    14. XM_054347848.1 → XP_054203823.1  polyamine-transporting ATPase 13A3 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y635, A0A2R8YDN7

    15. XM_054347856.1 → XP_054203831.1  polyamine-transporting ATPase 13A3 isoform X4

      UniProtKB/TrEMBL
      A0A2R8YDN7
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H7F0.4 GenPept UniProtKB/Swiss-Prot:Q9H7F0

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