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XKR9 XK related 9 [ Homo sapiens (human) ]

Gene ID: 389668, updated on 2-Nov-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, Nov 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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