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    XKR9 XK related 9 [ Homo sapiens (human) ]

    Gene ID: 389668, updated on 28-Oct-2024

    Summary

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    Official Symbol
    XKR9provided by HGNC
    Official Full Name
    XK related 9provided by HGNC
    Primary source
    HGNC:HGNC:20937
    See related
    Ensembl:ENSG00000221947 AllianceGenome:HGNC:20937
    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
    XRG9; hXKR9
    Summary
    Predicted to enable phospholipid scramblase activity. Predicted to be involved in apoptotic process involved in development; engulfment of apoptotic cell; and phosphatidylserine exposure on apoptotic cell surface. Predicted to be located in cell periphery and membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Broad expression in testis (RPKM 1.6), small intestine (RPKM 1.1) and 14 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See XKR9 in Genome Data Viewer
    Location:
    8q13.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (70669339..71065805)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (71099221..71495619)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (71581574..71648177)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19272 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19273 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19274 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19275 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27508 Neighboring gene LACTB2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27510 Neighboring gene translocation associated membrane protein 1 Neighboring gene RNA, 7SL, cytoplasmic 19, pseudogene Neighboring gene lactamase beta 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:71660008-71660508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27511 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:71716960-71717817 Neighboring gene uncharacterized LOC124901960 Neighboring gene NANOG hESC enhancer GRCh37_chr8:71971312-71971813 Neighboring gene uncharacterized LOC124901959 Neighboring gene uncharacterized LOC105375894 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:72117517-72118139 Neighboring gene EYA transcriptional coactivator and phosphatase 1

    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. Cryo-EM structures of the caspase-activated protein XKR9 involved in apoptotic lipid scrambling. Straub MS, et al. Elife, 2021 Jul 15. PMID 34263724, Free PMC Article
    2. Genome wide association study identifies two loci associated with cadmium in erythrocytes among never-smokers. Borné Y, et al. Hum Mol Genet, 2016 Jun 1. PMID 27005419
    3. Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. Estrada K, et al. Nat Genet, 2012 Apr 15. PMID 22504420, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    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

    EBI GWAS Catalog

    Description
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    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)

    Genotypes

    General gene information

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    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phospholipid scramblase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in apoptotic process involved in development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in engulfment of apoptotic cell IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phosphatidylserine exposure on apoptotic cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phosphatidylserine exposure on apoptotic cell surface ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    XK-related protein 9
    Names
    X Kell blood group precursor-related family, member 9
    X-linked Kx blood group related 9
    XK, Kell blood group complex subunit-related family, member 9

    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_001011720.2 → NP_001011720.1  XK-related protein 9 isoform 2

      See identical proteins and their annotated locations for NP_001011720.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 3. Variants 1, 3 and 4 encode the same isoform (2).
      Source sequence(s)
      AC022731, AY534247
      Consensus CDS
      CCDS34905.1
      UniProtKB/Swiss-Prot
      B2RNS9, B9EH74, Q5GH70
      Related
      ENSP00000386141.3, ENST00000408926.8
      Conserved Domains (1) summary
      pfam09815
      Location:10 → 346
      XK-related; XK-related protein

    2. NM_001287258.2 → NP_001274187.1  XK-related protein 9 isoform 1

      See identical proteins and their annotated locations for NP_001274187.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 3. It encodes isoform 1, which is shorter at the N-terminus, compared to isoform 2.
      Source sequence(s)
      AC022731, AY534247, BC111381
      UniProtKB/Swiss-Prot
      Q5GH70
      Conserved Domains (1) summary
      pfam09815
      Location:1 → 214
      XK-related; XK-related protein

    3. NM_001287259.2 → NP_001274188.1  XK-related protein 9 isoform 2

      See identical proteins and their annotated locations for NP_001274188.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) encodes the longer isoform (2). Variants 1, 3 and 4 encode the same protein.
      Source sequence(s)
      AC022731, AY534247, BC151845
      Consensus CDS
      CCDS34905.1
      UniProtKB/Swiss-Prot
      B2RNS9, B9EH74, Q5GH70
      Related
      ENSP00000431088.1, ENST00000520030.5
      Conserved Domains (1) summary
      pfam09815
      Location:10 → 346
      XK-related; XK-related protein

    4. NM_001287260.2 → NP_001274189.1  XK-related protein 9 isoform 2

      See identical proteins and their annotated locations for NP_001274189.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 3. Variants 1, 3 and 4 encode the same isoform (2).
      Source sequence(s)
      AC022731, AY534247, BC137105
      Consensus CDS
      CCDS34905.1
      UniProtKB/Swiss-Prot
      B2RNS9, B9EH74, Q5GH70
      Conserved Domains (1) summary
      pfam09815
      Location:10 → 346
      XK-related; XK-related 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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      70669339..71065805
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011517527.4 → XP_011515829.1  XK-related protein 9 isoform X3

      Conserved Domains (1) summary
      pfam09815
      Location:10 → 145
      XK-related; XK-related protein

    2. XM_011517525.3 → XP_011515827.1  XK-related protein 9 isoform X1

      See identical proteins and their annotated locations for XP_011515827.1

      UniProtKB/Swiss-Prot
      B2RNS9, B9EH74, Q5GH70
      Conserved Domains (1) summary
      pfam09815
      Location:10 → 346
      XK-related; XK-related protein

    3. XM_011517524.4 → XP_011515826.1  XK-related protein 9 isoform X1

      See identical proteins and their annotated locations for XP_011515826.1

      UniProtKB/Swiss-Prot
      B2RNS9, B9EH74, Q5GH70
      Conserved Domains (1) summary
      pfam09815
      Location:10 → 346
      XK-related; XK-related protein

    4. XM_017013405.3 → XP_016868894.1  XK-related protein 9 isoform X4

    5. XM_011517526.4 → XP_011515828.1  XK-related protein 9 isoform X2

      Conserved Domains (1) summary
      pfam09815
      Location:10 → 145
      XK-related; XK-related protein

    6. XM_017013404.3 → XP_016868893.1  XK-related protein 9 isoform X1

      UniProtKB/Swiss-Prot
      B2RNS9, B9EH74, Q5GH70
      Conserved Domains (1) summary
      pfam09815
      Location:10 → 346
      XK-related; XK-related protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      71099221..71495619
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054360457.1 → XP_054216432.1  XK-related protein 9 isoform X1

      UniProtKB/Swiss-Prot
      B2RNS9, B9EH74, Q5GH70

    2. XM_054360460.1 → XP_054216435.1  XK-related protein 9 isoform X3

    3. XM_054360461.1 → XP_054216436.1  XK-related protein 9 isoform X4

    4. XM_054360459.1 → XP_054216434.1  XK-related protein 9 isoform X2

    5. XM_054360456.1 → XP_054216431.1  XK-related protein 9 isoform X1

      UniProtKB/Swiss-Prot
      B2RNS9, B9EH74, Q5GH70

    6. XM_054360458.1 → XP_054216433.1  XK-related protein 9 isoform X1

      UniProtKB/Swiss-Prot
      B2RNS9, B9EH74, Q5GH70
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5GH70.1 GenPept UniProtKB/Swiss-Prot:Q5GH70

    Gene LinkOut

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