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    KXD1 KxDL motif containing 1 [ Homo sapiens (human) ]

    Gene ID: 79036, updated on 27-Nov-2024

    Summary

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    Official Symbol
    KXD1provided by HGNC
    Official Full Name
    KxDL motif containing 1provided by HGNC
    Primary source
    HGNC:HGNC:28420
    See related
    Ensembl:ENSG00000105700 MIM:615178; AllianceGenome:HGNC:28420
    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
    KXDL; BORCS4; MST096; MSTP096; C10orf50; C19orf50
    Summary
    Involved in lysosome localization. Part of BORC complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 13.1), placenta (RPKM 13.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KXD1 in Genome Data Viewer
    Location:
    19p13.11
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (18557870..18569378)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (18692823..18704439)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (18668680..18680188)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18557131-18557659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18561006-18561812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18561813-18562619 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18566359-18566575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14321 Neighboring gene elongation factor for RNA polymerase II Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18579531-18580168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10403 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18587281-18588108 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18589364-18590266 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:18594428-18594928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:18594929-18595429 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18596277-18596862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18605831-18606730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14323 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18611236-18612222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18618231-18619072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10405 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18631869-18632384 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18632385-18632900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18640318-18641203 Neighboring gene Sharpr-MPRA regulatory region 11651 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18652136-18652636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10407 Neighboring gene FKBP prolyl isomerase 8 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:18667707-18668498 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:18668499-18669288 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18672913-18673498 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18682001-18682677 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:18683356-18684032 Neighboring gene ubiquitin A-52 residue ribosomal protein fusion product 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18702459-18702982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18703866-18704367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10411 Neighboring gene Sharpr-MPRA regulatory region 11645 Neighboring gene required for excision 1-B domain containing Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18716731-18717649 Neighboring gene cytokine receptor like factor 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
    • 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. BORC complex specific components and Kinesin-1 mediate autophagy evasion by the autophagy-resistant Mycobacterium tuberculosis Beijing strain. Tunganuntarat J, et al. Sci Rep, 2023 Jan 30. PMID 36717601, Free PMC Article
    2. Yeast homologues of three BLOC-1 subunits highlight KxDL proteins as conserved interactors of BLOC-1. Hayes MJ, et al. Traffic, 2011 Mar. PMID 21159114, Free PMC Article
    3. The BLOS1-interacting protein KXD1 is involved in the biogenesis of lysosome-related organelles. Yang Q, et al. Traffic, 2012 Aug. PMID 22554196, Free PMC Article
    4. Biogenesis of lysosome-related organelles complex-1 (BORC) regulates late endosomal/lysosomal size through PIKfyve-dependent phosphatidylinositol-3,5-bisphosphate. Yordanov TE, et al. Traffic, 2019 Sep. PMID 31314175, Free PMC Article
    5. BORC, a multisubunit complex that regulates lysosome positioning. Pu J, et al. Dev Cell, 2015 Apr 20. PMID 25898167, Free PMC Article

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. BORC complex specific components and Kinesin-1 mediate autophagy evasion by the autophagy-resistant Mycobacterium tuberculosis Beijing strain.
      Title: BORC complex specific components and Kinesin-1 mediate autophagy evasion by the autophagy-resistant Mycobacterium tuberculosis Beijing strain.
    2. KXD1 interacts with BLOS1.
      Title: The BLOS1-interacting protein KXD1 is involved in the biogenesis of lysosome-related organelles.
    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

    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
    Knockdown of KxDL motif containing 1 (KXD1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC2749, FLJ25480, FLJ43375, DKFZp686B1038

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in lysosome localization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in lysosome localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lysosome localization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in organelle transport along microtubule NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of endosome size NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of lysosome size NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in vesicle-mediated transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of BLOC-1 complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of BORC complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of BORC complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of BORC complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytoplasmic side of lysosomal membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    kxDL motif-containing protein 1
    Names
    BLOC-1 related complex subunit 4
    UPF0459 protein C19orf50

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001171948.2 → NP_001165419.1  kxDL motif-containing protein 1

      See identical proteins and their annotated locations for NP_001165419.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, and 3 encode the same protein.
      Source sequence(s)
      AC005253, AK098346, DA542130
      Consensus CDS
      CCDS12381.1
      UniProtKB/Swiss-Prot
      O76098, Q9BQD3
      UniProtKB/TrEMBL
      M0QXP3
      Related
      ENSP00000443549.1, ENST00000540691.5
      Conserved Domains (1) summary
      pfam10241
      Location:14 → 93
      KxDL; Uncharacterized conserved protein

    2. NM_001171949.2 → NP_001165420.1  kxDL motif-containing protein 1

      See identical proteins and their annotated locations for NP_001165420.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein.
      Source sequence(s)
      AC005253, AK098346, BM781878, DA616317
      Consensus CDS
      CCDS12381.1
      UniProtKB/Swiss-Prot
      O76098, Q9BQD3
      UniProtKB/TrEMBL
      M0QXP3
      Related
      ENSP00000438903.1, ENST00000539106.5
      Conserved Domains (1) summary
      pfam10241
      Location:14 → 93
      KxDL; Uncharacterized conserved protein

    3. NM_024069.4 → NP_076974.2  kxDL motif-containing protein 1

      See identical proteins and their annotated locations for NP_076974.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein.
      Source sequence(s)
      AC005253, AK098346
      Consensus CDS
      CCDS12381.1
      UniProtKB/Swiss-Prot
      O76098, Q9BQD3
      UniProtKB/TrEMBL
      M0QXP3
      Related
      ENSP00000222307.3, ENST00000222307.9
      Conserved Domains (1) summary
      pfam10241
      Location:14 → 93
      KxDL; Uncharacterized conserved 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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      18557870..18569378
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017027281.2 → XP_016882770.1  kxDL motif-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      O76098, Q9BQD3
      UniProtKB/TrEMBL
      M0QXP3
      Related
      ENSP00000472836.1, ENST00000602094.5
      Conserved Domains (1) summary
      pfam10241
      Location:14 → 93
      KxDL; Uncharacterized conserved protein

    2. XM_047439389.1 → XP_047295345.1  kxDL motif-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      O76098, Q9BQD3

    3. XM_011528272.3 → XP_011526574.1  kxDL motif-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_011526574.1

      UniProtKB/Swiss-Prot
      O76098, Q9BQD3
      UniProtKB/TrEMBL
      M0QXP3
      Related
      ENSP00000469294.1, ENST00000597438.5
      Conserved Domains (1) summary
      pfam10241
      Location:14 → 93
      KxDL; Uncharacterized conserved protein

    4. XM_047439390.1 → XP_047295346.1  kxDL motif-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      O76098, Q9BQD3

    5. XM_047439388.1 → XP_047295344.1  kxDL motif-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      O76098, Q9BQD3

    6. XM_006722883.3 → XP_006722946.1  kxDL motif-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006722946.1

      UniProtKB/Swiss-Prot
      O76098, Q9BQD3
      UniProtKB/TrEMBL
      M0QXP3
      Related
      ENSP00000471554.1, ENST00000595073.5
      Conserved Domains (1) summary
      pfam10241
      Location:14 → 93
      KxDL; Uncharacterized conserved protein

    7. XM_017027282.2 → XP_016882771.1  kxDL motif-containing protein 1 isoform X2

      Conserved Domains (1) summary
      pfam10241
      Location:14 → 85
      KxDL; Uncharacterized conserved protein

    8. XM_005260073.5 → XP_005260130.1  kxDL motif-containing protein 1 isoform X2

      Conserved Domains (1) summary
      pfam10241
      Location:14 → 85
      KxDL; Uncharacterized conserved protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      18692823..18704439
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322063.1 → XP_054178038.1  kxDL motif-containing protein 1 isoform X1

    2. XM_054322061.1 → XP_054178036.1  kxDL motif-containing protein 1 isoform X1

    3. XM_054322059.1 → XP_054178034.1  kxDL motif-containing protein 1 isoform X1

    4. XM_054322064.1 → XP_054178039.1  kxDL motif-containing protein 1 isoform X1

    5. XM_054322062.1 → XP_054178037.1  kxDL motif-containing protein 1 isoform X1

    6. XM_054322060.1 → XP_054178035.1  kxDL motif-containing protein 1 isoform X1

    7. XM_054322065.1 → XP_054178040.1  kxDL motif-containing protein 1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BQD3.2 GenPept UniProtKB/Swiss-Prot:Q9BQD3

    Gene LinkOut

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