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

Gene ID: 79036, updated on 3-Apr-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, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 13.1), placenta (RPKM 13.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
19p13.11
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (18557870..18569378)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (18692823..18704439)
105.20220307 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 (29) 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)

Genotypes

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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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_2023_10

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

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