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

Gene ID: 80700, updated on 10-Oct-2024

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. Is extrinsic component of membrane. Part of endosome and protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 49.0), kidney (RPKM 36.6) and 25 other tissues See more
Orthologs
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Genomic context

See UBXN6 in Genome Data Viewer
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_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4350305-4350806 Neighboring gene eukaryotic translation initiation factor 1 pseudogene 6 Neighboring gene MPN domain containing Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4365919-4366840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4368989-4369938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4369939-4370886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4372431-4373164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4373165-4373898 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr19:4374633-4375365 and GRCh37_chr19:4375366-4376099 Neighboring gene SH3 domain containing GRB2 like 1, endophilin A2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4377567-4378299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13773 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:4386482-4386982 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4389401-4390008 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4390009-4390615 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4390616-4391224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4394991-4395501 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4399905-4400734 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4402397-4403094 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4403095-4403790 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4408505-4409316 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4409317-4410128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4412803-4413801 Neighboring gene chromatin assembly factor 1 subunit A Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:4430727-4431490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4436676-4437176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4437177-4437677 Neighboring gene Sharpr-MPRA regulatory region 9621 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:4444373-4444541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4453327-4454026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13774 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9891 Neighboring gene microRNA 4746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9893 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4474209-4475158 Neighboring gene HDGF like 2 Neighboring gene perilipin 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4534387-4534942 Neighboring gene perilipin 5

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ00394, DKFZp667D109

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 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

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)

  1. NM_001171091.2NP_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:105210
    PUB_UBXD1; PNGase/UBA or UBX (PUB) domain of UBXD1
    cl00155
    Location:281354
    UBQ; Ubiquitin-like proteins
  2. NM_025241.3NP_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:158263
    PUB_UBXD1; PNGase/UBA or UBX (PUB) domain of UBXD1
    PHA00003
    Location:63103
    B; internal scaffolding protein
    cl00155
    Location:334407
    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

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    4445006..4457879 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    4428463..4442199 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322231.1XP_054178206.1  UBX domain-containing protein 6 isoform X3

  2. XM_054322232.1XP_054178207.1  UBX domain-containing protein 6 isoform X4

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