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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
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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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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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