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

    Gene ID: 80700, updated on 7-Jul-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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See UBXN6 in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (4445006..4457879, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (4428463..4442199, complement)
    105.20220307 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
    • 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)

    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_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_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
      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

      UniProtKB/TrEMBL
      K7EP32
      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

      UniProtKB/TrEMBL
      K7EP32
    3. XM_054322233.1XP_054178208.1  UBX domain-containing protein 6 isoform X5