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    UBTD2 ubiquitin domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 92181, updated on 5-Mar-2024

    Summary

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    Official Symbol
    UBTD2provided by HGNC
    Official Full Name
    ubiquitin domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:24463
    See related
    Ensembl:ENSG00000168246 MIM:610174; AllianceGenome:HGNC:24463
    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
    DCUBP
    Summary
    Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 21.6), endometrium (RPKM 12.8) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    5q35.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (172209646..172284117, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (172749942..172824384, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (171636650..171710768, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171481332-171482159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171482181-171482682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171482683-171483182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23620 Neighboring gene serine/threonine kinase 10 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171528850-171529636 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171542101-171542601 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171571210-171571710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23624 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:171578576-171578751 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171591501-171592480 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:171602275-171602501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23625 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171606399-171607102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16618 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:171615213-171615988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23630 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23631 Neighboring gene EF-hand calcium binding domain 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23632 Neighboring gene small nucleolar RNA SNORA57 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:171710845-171711445 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:171711446-171712045 Neighboring gene uncharacterized LOC100288254 Neighboring gene KLF3 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171762901-171763762 Neighboring gene SH3 and PX domains 2B Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:171788418-171789617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23637 Neighboring gene MPRA-validated peak5578 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171839705-171840206 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171845006-171845982 Neighboring gene Sharpr-MPRA regulatory region 10478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171858257-171858757 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:171859347-171859604 Neighboring gene Sharpr-MPRA regulatory region 6627 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:171880495-171881016

    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. Solution structure of the ubiquitin-like domain of human DC-UbP from dendritic cells. Gao YG, et al. Protein Sci, 2005 Aug. PMID 15987890, Free PMC Article
    2. Cloning and identification of a novel human ubiquitin-like protein, DC-UbP, from dendritic cells. Liu S, et al. Biochem Biophys Res Commun, 2003 Jan 17. PMID 12507522
    3. Solution structure of the N-terminal domain of DC-UbP/UBTD2 and its interaction with ubiquitin. Song AX, et al. Protein Sci, 2010 May. PMID 20440844, Free PMC Article
    4. A ubiquitin shuttle DC-UbP/UBTD2 reconciles protein ubiquitination and deubiquitination via linking UbE1 and USP5 enzymes. Song AX, et al. PLoS One, 2014. PMID 25207809, Free PMC Article
    5. The DNA sequence and comparative analysis of human chromosome 5. Schmutz J, et al. Nature, 2004 Sep 16. PMID 15372022

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A ubiquitin shuttle DC-UbP reconciles protein ubiquitination and deubiquitination via linking UbE1 and USP5 enzymes.
      Title: A ubiquitin shuttle DC-UbP/UBTD2 reconciles protein ubiquitination and deubiquitination via linking UbE1 and USP5 enzymes.
    2. The results show that DC-UbP_N holds a novel structural fold and acts as a Ub-binding domain (UBD) but with low affinity.
      Title: Solution structure of the N-terminal domain of DC-UbP/UBTD2 and its interaction with ubiquitin.
    3. cloning and identification; DC-UbP might be downregulated during cellular differentiation and apoptosis
      Title: Cloning and identification of a novel human ubiquitin-like protein, DC-UbP, from dendritic cells.
    4. Solution NMR structure of the ubiquitin-like domain of DC-UbP is very similar to that of ubiquitin despite low similarity (<30%) in amino-acid sequence.
      Title: Solution structure of the ubiquitin-like domain of human DC-UbP from dendritic cells.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC30022

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin domain-containing protein 2
    Names
    ubiquitin-like protein SB72

    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_152277.3 → NP_689490.2  ubiquitin domain-containing protein 2

      See identical proteins and their annotated locations for NP_689490.2

      Status: VALIDATED

      Source sequence(s)
      AC008671, AC024561
      Consensus CDS
      CCDS4379.2
      UniProtKB/Swiss-Prot
      Q8TDQ3, Q8WUN7
      Related
      ENSP00000377381.2, ENST00000393792.3
      Conserved Domains (2) summary
      cd17121
      Location:151 → 225
      Ubl_UBTD2; ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 2 (UBTD2)
      pfam16455
      Location:30 → 132
      UBD; Ubiquitin-binding domain

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      172209646..172284117 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417875.1 → XP_047273831.1  ubiquitin domain-containing protein 2 isoform X1

      UniProtKB/TrEMBL
      B2R886

    2. XM_047417876.1 → XP_047273832.1  ubiquitin domain-containing protein 2 isoform X1

      UniProtKB/TrEMBL
      B2R886

    3. XM_017010022.2 → XP_016865511.1  ubiquitin domain-containing protein 2 isoform X1

      UniProtKB/TrEMBL
      B2R886
      Conserved Domains (2) summary
      cd17121
      Location:107 → 181
      Ubl_UBTD2; ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 2 (UBTD2)
      pfam16455
      Location:1 → 88
      UBD; Ubiquitin-binding domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      172749942..172824384 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353795.1 → XP_054209770.1  ubiquitin domain-containing protein 2 isoform X1

      UniProtKB/TrEMBL
      B2R886

    2. XM_054353793.1 → XP_054209768.1  ubiquitin domain-containing protein 2 isoform X1

      UniProtKB/TrEMBL
      B2R886

    3. XM_054353794.1 → XP_054209769.1  ubiquitin domain-containing protein 2 isoform X1

      UniProtKB/TrEMBL
      B2R886
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WUN7.2 GenPept UniProtKB/Swiss-Prot:Q8WUN7

    Gene LinkOut

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