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    XPR1 xenotropic and polytropic retrovirus receptor 1 [ Homo sapiens (human) ]

    Gene ID: 9213, updated on 17-Jun-2024

    Summary

    Official Symbol
    XPR1provided by HGNC
    Official Full Name
    xenotropic and polytropic retrovirus receptor 1provided by HGNC
    Primary source
    HGNC:HGNC:12827
    See related
    Ensembl:ENSG00000143324 MIM:605237; AllianceGenome:HGNC:12827
    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
    X3; SYG1; IBGC6; SLC53A1
    Summary
    The protein encoded by this gene is a receptor for the xenotropic and polytropic classes of murine leukemia viruses. The encoded protein is involved in phosphate homeostasis by mediating phosphate export from the cell. Defects in this gene have been associated with idiopathic basal ganglia calcification-6. [provided by RefSeq, Jun 2016]
    Expression
    Ubiquitous expression in heart (RPKM 12.0), testis (RPKM 8.5) and 24 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See XPR1 in Genome Data Viewer
    Location:
    1q25.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (180632022..180890279)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (179987035..180245477)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (180601158..180859415)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene acyl-CoA binding domain containing 6 Neighboring gene microRNA 3121 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:180470119-180470634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:180470635-180471150 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:180471258-180471758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2164 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:180490465-180491664 Neighboring gene uncharacterized LOC124904658 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:180540570-180541769 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:180555052-180555235 Neighboring gene CRISPRi-validated cis-regulatory element chr1.10130 Neighboring gene ovarian adenocarcinoma amplified long non-coding RNA Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:180601022-180601522 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:180601523-180602023 Neighboring gene MPRA-validated peak486 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:180679967-180680667 Neighboring gene uncharacterized LOC124904687 Neighboring gene MPRA-validated peak488 silencer Neighboring gene MPRA-validated peak489 silencer Neighboring gene uncharacterized LOC124904464 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:180866978-180867370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:180868044-180868872 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1596 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2165 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:180892213-180893094 Neighboring gene long intergenic non-protein coding RNA 2816 Neighboring gene uncharacterized LOC107985231 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:180910063-180911042 Neighboring gene KIAA1614

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Basal ganglia calcification, idiopathic, 6 Compare labs

    EBI GWAS Catalog

    Description
    Rank-based genome-wide analysis reveals the association of ryanodine receptor-2 gene variants with childhood asthma among human populations.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ90308

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables efflux transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables inositol hexakisphosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables inositol hexakisphosphate binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phosphate transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables phosphate transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables virus receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in cellular response to phosphate starvation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in intracellular phosphate ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in phosphate ion transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in phosphate ion transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in response to virus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in symbiont entry into host cell IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
    PubMed 

    General protein information

    Preferred Names
    solute carrier family 53 member 1
    Names
    X-receptor
    phosphate exporter SLC53A1
    protein SYG1 homolog
    solute carrier family 53 (phosphate exporter), member 1
    xenotropic and polytropic murine leukemia virus receptor X3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_050964.1 RefSeqGene

      Range
      5013..263270
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001135669.2NP_001129141.1  solute carrier family 53 member 1 isoform 2

      See identical proteins and their annotated locations for NP_001129141.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AA425354, AL162431, BC041142, DB461474
      Consensus CDS
      CCDS44284.1
      UniProtKB/Swiss-Prot
      Q9UBH6
      Related
      ENSP00000356561.3, ENST00000367589.3
      Conserved Domains (2) summary
      cd14477
      Location:2165
      SPX_XPR1_like; SPX domain of the xenotropic and polytropic retrovirus receptor 1 (XPR1) and related proteins
      pfam03124
      Location:268552
      EXS; EXS family
    2. NM_001328662.2NP_001315591.1  solute carrier family 53 member 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL358434, AL590085
    3. NM_004736.4NP_004727.2  solute carrier family 53 member 1 isoform 1

      See identical proteins and their annotated locations for NP_004727.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA425354, AF115389, AL162431, BC041142, DB461474
      Consensus CDS
      CCDS1340.1
      UniProtKB/Swiss-Prot
      O95719, Q7L8K9, Q8IW20, Q9NT19, Q9UBH6, Q9UFB9
      Related
      ENSP00000356562.4, ENST00000367590.9
      Conserved Domains (2) summary
      cd14477
      Location:2165
      SPX_XPR1_like; SPX domain of the xenotropic and polytropic retrovirus receptor 1 (XPR1) and related proteins
      pfam03124
      Location:268617
      EXS; EXS family

    RNA

    1. NR_137330.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two alternate exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL162431, AL358434, AL590085

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      180632022..180890279
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      179987035..180245477
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)