UBXN6 UBX domain protein 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: UBXN6provided by HGNC
Official Full Name: UBX domain protein 6provided by HGNC
Primary source: HGNC:HGNC:14928
See related: Ensembl:ENSG00000167671 MIM:611946; AllianceGenome:HGNC:14928
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: UBXD1; UBXDC2
Summary: Involved in ERAD pathway; endosome to lysosome transport via multivesicular body sorting pathway; and macroautophagy. Located in bounding membrane of organelle and cytosol. Part of endosome and protein-containing complex. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in testis (RPKM 49.0), kidney (RPKM 36.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19p13.3

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (4445006..4457879, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (4428463..4442199, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (4445003..4457791, complement)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

UBX Domain Protein 6 Positively Regulates JAK-STAT1/2 Signaling.
Title: UBX Domain Protein 6 Positively Regulates JAK-STAT1/2 Signaling.
Structure of the PUB Domain from Ubiquitin Regulatory X Domain Protein 1 (UBXD1) and Its Interaction with the p97 AAA+ ATPase.
Title: Structure of the PUB Domain from Ubiquitin Regulatory X Domain Protein 1 (UBXD1) and Its Interaction with the p97 AAA+ ATPase.
In HIV-positive long-term non-progressors, a higher prevalence of Ala31Thr in UBXN6 was found within its N-terminal region
Title: Association of a single nucleotide polymorphism in the ubxn6 gene with long-term non-progression phenotype in HIV-positive individuals.
UBXD1 as mitochondrial recruitment factor for p97 further connects the ubiquitin-proteasome system to Parkin-dependent mitophagy and underlines the close cooperation between the different mechanisms involved in mitochondrial maintenance.
Title: UBXD1 is a mitochondrial recruitment factor for p97/VCP and promotes mitophagy.
These results indicate that the outer membrane protein MCL1 is degraded by the VCP-UBXD1 complex and that the process is promoted by the presence of mutant Huntingtin.
Title: VCP cooperates with UBXD1 to degrade mitochondrial outer membrane protein MCL1 in model of Huntington's disease.
Upon damage, p97 translocates to lysosomes and there cooperates with a distinct set of cofactors including UBXD1, PLAA, and the deubiquitinating enzyme YOD1, which we term ELDR components for Endo-Lysosomal Damage Response.
Title: VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy.
UBXD1-N intercalates into the p97-ND1 interface, thereby modulating interdomain communication of p97 domains and its activity with relevance for disease pathogenesis
Title: The N-terminal Region of the Ubiquitin Regulatory X (UBX) Domain-containing Protein 1 (UBXD1) Modulates Interdomain Communication within the Valosin-containing Protein p97.
Data indicate that endosomal trafficking of CAV1 depends on ubiquitination of the N-terminal region and the subsequent recruitment of VCP-UBXD1.
Title: Ubiquitination of the N-terminal region of caveolin-1 regulates endosomal sorting by the VCP/p97 AAA-ATPase.
UBXD1 modulates the trafficking of ERGIC-53-containing vesicles by controlling the interaction of transport factors with the cytoplasmic tail of ERGIC-53.
Title: Protein interaction profiling of the p97 adaptor UBXD1 points to a role for the complex in modulating ERGIC-53 trafficking.
Data show that expression of VCP mutant proteins, or siRNA-mediated depletion of UBXD1 leads to a block of CAV1 transport at the limiting membrane of enlarged endosomes in cultured cells.
Title: Endolysosomal sorting of ubiquitylated caveolin-1 is regulated by VCP and UBXD1 and impaired by VCP disease mutations.

Submit: New GeneRIF Correction See all GeneRIFs (13)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH80339 (e-PCR)
- UniSTS:87852

RH78272 (e-PCR)
- UniSTS:59462

RH67001 (e-PCR)
- UniSTS:92775

G42939 (e-PCR)
- UniSTS:94834

G34951 (e-PCR)
- UniSTS:117661

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 ERAD pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endosome to lysosome transport via multivesicular body sorting pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in macroautophagy	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in centrosome	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in late endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: UBX domain-containing protein 6

Names: CTB-50L17.16; UBX domain containing 1; UBX domain-containing 2; UBX domain-containing protein 1

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)

NM_001171091.2 → NP_001164562.1 UBX domain-containing protein 6 isoform 2

See identical proteins and their annotated locations for NP_001164562.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) has an alternate 5' exon, resulting in a downstream in-frame AUG start codon, as compared to variant 1. The resulting isoform (2) is shorter than isoform 1 at the N-terminus.

Source sequence(s)

AC011498, AF272894, BC007414, BC008288

Consensus CDS

CCDS54201.1

UniProtKB/TrEMBL

K7EP32

Related

ENSP00000378246.2, ENST00000394765.7

Conserved Domains (2) summary

cd10460
Location:105 → 210

PUB_UBXD1; PNGase/UBA or UBX (PUB) domain of UBXD1

cl00155
Location:281 → 354

UBQ; Ubiquitin-like proteins
NM_025241.3 → NP_079517.1 UBX domain-containing protein 6 isoform 1

See identical proteins and their annotated locations for NP_079517.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

BC007414, BC008288, BM764980

Consensus CDS

CCDS12129.1

UniProtKB/Swiss-Prot

D6W626, Q96AH1, Q96IK9, Q9BZV0, Q9BZV1

UniProtKB/TrEMBL

K7EP32

Related

ENSP00000301281.5, ENST00000301281.11

Conserved Domains (3) summary

cd10460
Location:158 → 263

PUB_UBXD1; PNGase/UBA or UBX (PUB) domain of UBXD1

PHA00003
Location:63 → 103

B; internal scaffolding protein

cl00155
Location:334 → 407

UBQ; Ubiquitin-like proteins

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

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

4445006..4457879 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017027325.2 → XP_016882814.2 UBX domain-containing protein 6 isoform X1

UniProtKB/TrEMBL

K7EP32

Related

ENSP00000467206.1, ENST00000591919.5
XM_047439470.1 → XP_047295426.1 UBX domain-containing protein 6 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

4428463..4442199 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054322231.1 → XP_054178206.1 UBX domain-containing protein 6 isoform X3
XM_054322232.1 → XP_054178207.1 UBX domain-containing protein 6 isoform X4

UniProtKB/TrEMBL

K7EP32
XM_054322233.1 → XP_054178208.1 UBX domain-containing protein 6 isoform X5