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UBFD1 ubiquitin family domain containing 1 [ Homo sapiens (human) ]

Gene ID: 56061, updated on 5-May-2024

Summary

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Official Symbol
UBFD1provided by HGNC
Official Full Name
ubiquitin family domain containing 1provided by HGNC
Primary source
HGNC:HGNC:30565
See related
Ensembl:ENSG00000103353 AllianceGenome:HGNC:30565
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
UBPH
Summary
Enables RNA binding activity and cadherin binding activity. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 14.6), thyroid (RPKM 8.8) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16p12.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (23557727..23574389)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (23833526..23850188)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (23569048..23585710)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene golgi associated, gamma adaptin ear containing, ARF binding protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:23511811-23512473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23515779-23516280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23516281-23516780 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7277 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7278 Neighboring gene cyclin Y like 7 (pseudogene) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10582 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:23549327-23549828 Neighboring gene glutamyl-tRNA synthetase 2, mitochondrial Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:23549829-23550328 Neighboring gene SUB1 pseudogene 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:23567356-23568000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10583 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:23568645-23569289 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:23569290-23569933 Neighboring gene NADH:ubiquinone oxidoreductase subunit AB1 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:23605373-23605549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7281 Neighboring gene partner and localizer of BRCA2 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:23651698-23651932

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. Identification of polyubiquitin binding proteins involved in NF-kappaB signaling using protein arrays. Fenner BJ, et al. Biochim Biophys Acta, 2009 Jul. PMID 19285159
  2. Autoubiquitination of the 26S proteasome on Rpn13 regulates breakdown of ubiquitin conjugates. Besche HC, et al. EMBO J, 2014 May 16. PMID 24811749, Free PMC Article
  3. Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. Loftus BJ, et al. Genomics, 1999 Sep 15. PMID 10493829
  4. Systematic identification of cancer cell vulnerabilities to natural killer cell-mediated immune surveillance. Pech MF, et al. Elife, 2019 Aug 27. PMID 31452512, Free PMC Article
  5. Proteomic Analysis of the EWS-Fli-1 Interactome Reveals the Role of the Lysosome in EWS-Fli-1 Turnover. Elzi DJ, et al. J Proteome Res, 2014 Aug 1. PMID 24999758, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

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

  • FLJ38870, FLJ42145

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables cadherin binding HDA PubMed 

General protein information

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Preferred Names
ubiquitin domain-containing protein UBFD1
Names
ubiquitin-binding protein homolog

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_019116.3 → NP_061989.2  ubiquitin domain-containing protein UBFD1

    See identical proteins and their annotated locations for NP_061989.2

    Status: VALIDATED

    Source sequence(s)
    AC008870, AK092696
    Consensus CDS
    CCDS10613.2
    UniProtKB/Swiss-Prot
    A8MW58, D3DWF2, O14562
    UniProtKB/TrEMBL
    H3BRL3
    Related
    ENSP00000379217.3, ENST00000395878.8
    Conserved Domains (2) summary
    smart00213
    Location:86 → 155
    UBQ; Ubiquitin homologues
    pfam00240
    Location:89 → 156
    ubiquitin; Ubiquitin family

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    23557727..23574389
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545894.4 → XP_011544196.1  ubiquitin domain-containing protein UBFD1 isoform X2

    Conserved Domains (2) summary
    smart00213
    Location:86 → 155
    UBQ; Ubiquitin homologues
    pfam00240
    Location:89 → 156
    ubiquitin; Ubiquitin family

  2. XM_047434367.1 → XP_047290323.1  ubiquitin domain-containing protein UBFD1 isoform X4

  3. XM_017023459.3 → XP_016878948.1  ubiquitin domain-containing protein UBFD1 isoform X1

    UniProtKB/TrEMBL
    H3BRL3

  4. XM_017023460.3 → XP_016878949.1  ubiquitin domain-containing protein UBFD1 isoform X3

    UniProtKB/TrEMBL
    H3BRL3
    Related
    ENST00000571064.5

RNA

  1. XR_007064893.1 RNA Sequence

    Related
    ENST00000567264.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    23833526..23850188
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054313495.1 → XP_054169470.1  ubiquitin domain-containing protein UBFD1 isoform X2

  2. XM_054313497.1 → XP_054169472.1  ubiquitin domain-containing protein UBFD1 isoform X4

  3. XM_054313494.1 → XP_054169469.1  ubiquitin domain-containing protein UBFD1 isoform X1

  4. XM_054313496.1 → XP_054169471.1  ubiquitin domain-containing protein UBFD1 isoform X3

RNA

  1. XR_008484709.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14562.2 GenPept UniProtKB/Swiss-Prot:O14562

Gene LinkOut

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