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

    Gene ID: 56061, updated on 10-Dec-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, Dec 2024]
    Expression
    Ubiquitous expression in testis (RPKM 14.6), thyroid (RPKM 8.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See UBFD1 in Genome Data Viewer
    Location:
    16p12.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (23557727..23574389)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (23833526..23850188)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. Binding of USP4 to cortactin enhances cell migration in HCT116 human colon cancer cells. Yun SI, et al. FASEB J, 2023 May. PMID 37039823
    5. Proximity labeling of endogenous RICTOR identifies mTOR complex 2 regulation by ADP ribosylation factor ARF1. Luciano AK, et al. J Biol Chem, 2022 Oct. PMID 35973513, Free PMC Article

    See all (32) 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)

    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_2024_08

    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

      UniProtKB/TrEMBL
      H3BRL3

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

      UniProtKB/TrEMBL
      H3BRL3

    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

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