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    UBASH3A ubiquitin associated and SH3 domain containing A [ Homo sapiens (human) ]

    Gene ID: 53347, updated on 3-Apr-2024

    Summary

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    Official Symbol
    UBASH3Aprovided by HGNC
    Official Full Name
    ubiquitin associated and SH3 domain containing Aprovided by HGNC
    Primary source
    HGNC:HGNC:12462
    See related
    Ensembl:ENSG00000160185 MIM:605736; AllianceGenome:HGNC:12462
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TULA; CLIP4; STS-2; TULA-1
    Summary
    This gene encodes one of two family members belonging to the T-cell ubiquitin ligand (TULA) family. Both family members can negatively regulate T-cell signaling. This family member can facilitate growth factor withdrawal-induced apoptosis in T cells, which may occur via its interaction with AIF, an apoptosis-inducing factor. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]
    Expression
    Biased expression in lymph node (RPKM 3.3), appendix (RPKM 1.9) and 12 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    21q22.3
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (42403902..42447684)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (40793440..40837215)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (43824011..43867794)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372815 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13342 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:43787692-43788891 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43789597-43790587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43792792-43793740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43796799-43797369 Neighboring gene trefoil factor 1 Neighboring gene transmembrane serine protease 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43808797-43809682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18513 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:43814254-43815453 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:43834765-43835964 Neighboring gene RNA, U6 small nuclear 1149, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43857898-43858585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43858586-43859272 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18517 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43883987-43884498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18518 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:43887967-43889166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18521 Neighboring gene radial spoke head component 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:43912470-43913669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13344 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13345 Neighboring gene RSPH1 divergent transcript

    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. UBASH3A gene polymorphisms and expression profile in rheumatoid arthritis. Yang XK, et al. Autoimmunity, 2019 Feb. PMID 30822156
    2. Association of UBASH3A gene polymorphism and atopic dermatitis in the Chinese Han population. Li Y, et al. Genes Immun, 2017 Sep. PMID 28747736
    3. Decreased UBASH3A mRNA Expression Levels in Peripheral Blood Mononuclear Cells from Patients with Systemic Lupus Erythematosus. Liu J, et al. Inflammation, 2015 Oct. PMID 25876712
    4. Association of UBASH3A gene polymorphisms and systemic lupus erythematosus in a Chinese population. Liu J, et al. Gene, 2015 Jul 1. PMID 25843625
    5. Lack of association between polymorphisms in the UBASH3A gene and autoimmune thyroid disease: a case control study. Cai T, et al. Arq Bras Endocrinol Metabol, 2014 Aug. PMID 25211447

    See all (52) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FLI1 induces erythroleukemia through opposing effects on UBASH3A and UBASH3B expression.
      Title: FLI1 induces erythroleukemia through opposing effects on UBASH3A and UBASH3B expression.
    2. Replication of association at the LPP and UBASH3A loci in a UK autoimmune Addison's disease cohort.
      Title: Replication of association at the LPP and UBASH3A loci in a UK autoimmune Addison's disease cohort.
    3. CRKL, AIFM3, AIF, BCL2, and UBASH3A during Human Kidney Development.
      Title: CRKL, AIFM3, AIF, BCL2, and UBASH3A during Human Kidney Development.
    4. Upon TCR engagement, UBASH3A enhances the downmodulation of cell-surface TCR-CD3.
      Title: UBASH3A Regulates the Synthesis and Dynamics of TCR-CD3 Complexes.
    5. observations suggested that the dysregulation of UBASH3A might be associated with the pathogenesis of rheumatoid arthritis (RA), and UBASH3A gene polymorphisms (rs1893592 and rs3788013) might contribute to RA susceptibility in Chinese Han population.
      Title: UBASH3A gene polymorphisms and expression profile in rheumatoid arthritis.
    6. this reduction in UBASH3A, as a consequence of the minor allele at rs1893592, resulted in increased secretion of IL-2, a key cytokine that is required for T-cell activation and function but is deficient in some type 1 diabetes (T1D). Our study provides new mechanistic insights into how rs1893592 affects T1D and autoimmunity and how interactions between multiple T1D-associated, noncoding variants influence the disease risk
      Title: Molecular-genetic characterization of common, noncoding UBASH3A variants associated with type 1 diabetes.
    7. UBASH3A gene SNP is associated with susceptibility to atopic dermatitis in Chinese Han population.
      Title: Association of UBASH3A gene polymorphism and atopic dermatitis in the Chinese Han population.
    8. UBASH3A attenuates the NF-kappaB signal transduction upon T-cell receptor (TCR) stimulation by specifically suppressing the activation of the IkappaB kinase complex. UBASH3A interacts with TAK1 and NEMO, suggesting that UBASH3A regulates the NF-kappaB signaling pathway by an ubiquitin-dependent mechanism. T1D risk alleles at rs11203203 and rs80054410 increase UBASH3A expression in CD4(+) T cells upon TCR stimulation.
      Title: UBASH3A Mediates Risk for Type 1 Diabetes Through Inhibition of T-Cell Receptor-Induced NF-κB Signaling.
    9. A negative correlation was found between UBASH3A mRNA expression and systemic lupus erythematosus.
      Title: Decreased UBASH3A mRNA Expression Levels in Peripheral Blood Mononuclear Cells from Patients with Systemic Lupus Erythematosus.
    10. Findings suggest that UBASH3A gene might contribute to systemic lupus erythematosus susceptibility and influence the clinical phenotype of the disease.
      Title: Association of UBASH3A gene polymorphisms and systemic lupus erythematosus in a Chinese population.
    Submit: New GeneRIF Correction See all GeneRIFs (22)

    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

    EBI GWAS Catalog

    Description
    Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes.
    EBI GWAS Catalog
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog
    Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases.
    EBI GWAS Catalog
    Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.
    EBI GWAS Catalog
    Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
    EBI GWAS Catalog
    Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo.
    EBI GWAS Catalog

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of ubiquitin associated and SH3 domain containing A (UBASH3A) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag Expression of TULA proteins reduces the production of HIV-1 particles and modulates Gag processing. ABCE1 recruits TULA to Gag PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 negative regulation of T cell receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cytokine production IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol HDA PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin-associated and SH3 domain-containing protein A
    Names
    T-cell ubiquitin ligand 1
    T-cell ubiquitin ligand protein
    cbl-interacting protein 4
    suppressor of T-cell receptor signaling 2

    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.

    Genomic

    1. NG_029750.2 RefSeqGene

      Range
      5041..48823
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001001895.3 → NP_001001895.1  ubiquitin-associated and SH3 domain-containing protein A isoform 2

      See identical proteins and their annotated locations for NP_001001895.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (2, also known as short form) that is shorter than isoform 1.
      Source sequence(s)
      AA707211, AF521702, AJ277750, AP001624, DA926085
      Consensus CDS
      CCDS33566.1
      UniProtKB/TrEMBL
      A0A0U1RRC9
      Related
      ENSP00000291535.6, ENST00000291535.11
      Conserved Domains (4) summary
      cd11937
      Location:241 → 300
      SH3_UBASH3A; Src homology 3 domain of Ubiquitin-associated and SH3 domain-containing protein A
      cd14300
      Location:25 → 61
      UBA_UBS3A_like; UBA domain found in ubiquitin-associated and SH3 domain-containing protein A (UBS3A) and similar proteins
      pfam00300
      Location:412 → 574
      His_Phos_1; Histidine phosphatase superfamily (branch 1)
      cl11399
      Location:332 → 464
      HP; Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction

    2. NM_001243467.2 → NP_001230396.1  ubiquitin-associated and SH3 domain-containing protein A isoform 3

      See identical proteins and their annotated locations for NP_001230396.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, and two alternate exons that result in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AA707211, AJ277750, AP001624, BC069577, DA926085
      Consensus CDS
      CCDS58791.1
      UniProtKB/TrEMBL
      A0A0U1RRC9
      Related
      ENSP00000381408.1, ENST00000398367.1
      Conserved Domains (3) summary
      cd07067
      Location:360 → 475
      HP_PGM_like; Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction
      cd11937
      Location:241 → 300
      SH3_UBASH3A; Src homology 3 domain of Ubiquitin-associated and SH3 domain-containing protein A
      cd14300
      Location:25 → 61
      UBA_UBS3A_like; UBA domain found in ubiquitin-associated and SH3 domain-containing protein A (UBS3A) and similar proteins

    3. NM_018961.4 → NP_061834.1  ubiquitin-associated and SH3 domain-containing protein A isoform 1

      See identical proteins and their annotated locations for NP_061834.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1, also known as long form).
      Source sequence(s)
      AA707211, AJ277750, AP001624, DA926085
      Consensus CDS
      CCDS13687.1
      UniProtKB/Swiss-Prot
      G5E9E4, P57075, Q6HA34, Q6HA35, Q6ISI6, Q6ISK3, Q6ISS9
      Related
      ENSP00000317327.6, ENST00000319294.11
      Conserved Domains (4) summary
      cd11937
      Location:279 → 338
      SH3_UBASH3A; Src homology 3 domain of Ubiquitin-associated and SH3 domain-containing protein A
      cd14300
      Location:25 → 61
      UBA_UBS3A_like; UBA domain found in ubiquitin-associated and SH3 domain-containing protein A (UBS3A) and similar proteins
      pfam00300
      Location:450 → 612
      His_Phos_1; Histidine phosphatase superfamily (branch 1)
      cl11399
      Location:370 → 502
      HP; Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      42403902..42447684
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440831.1 → XP_047296787.1  ubiquitin-associated and SH3 domain-containing protein A isoform X1

    2. XM_047440833.1 → XP_047296789.1  ubiquitin-associated and SH3 domain-containing protein A isoform X3

    3. XM_047440832.1 → XP_047296788.1  ubiquitin-associated and SH3 domain-containing protein A isoform X2

    4. XM_047440836.1 → XP_047296792.1  ubiquitin-associated and SH3 domain-containing protein A isoform X6

    5. XM_047440834.1 → XP_047296790.1  ubiquitin-associated and SH3 domain-containing protein A isoform X4

    6. XM_047440837.1 → XP_047296793.1  ubiquitin-associated and SH3 domain-containing protein A isoform X6

    7. XM_011529609.3 → XP_011527911.1  ubiquitin-associated and SH3 domain-containing protein A isoform X8

      See identical proteins and their annotated locations for XP_011527911.1

      UniProtKB/TrEMBL
      A0A0U1RQY9
      Related
      ENSP00000489235.1, ENST00000473381.1
      Conserved Domains (3) summary
      cd07067
      Location:398 → 496
      HP_PGM_like; Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction
      cd11937
      Location:279 → 338
      SH3_UBASH3A; Src homology 3 domain of Ubiquitin-associated and SH3 domain-containing protein A
      cd14300
      Location:25 → 61
      UBA_UBS3A_like; UBA domain found in ubiquitin-associated and SH3 domain-containing protein A (UBS3A) and similar proteins

    8. XM_047440838.1 → XP_047296794.1  ubiquitin-associated and SH3 domain-containing protein A isoform X7

    9. XM_047440839.1 → XP_047296795.1  ubiquitin-associated and SH3 domain-containing protein A isoform X8

    10. XM_047440835.1 → XP_047296791.1  ubiquitin-associated and SH3 domain-containing protein A isoform X5

    11. XM_047440840.1 → XP_047296796.1  ubiquitin-associated and SH3 domain-containing protein A isoform X9

    RNA

    1. XR_007067789.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      40793440..40837215
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324558.1 → XP_054180533.1  ubiquitin-associated and SH3 domain-containing protein A isoform X1

    2. XM_054324560.1 → XP_054180535.1  ubiquitin-associated and SH3 domain-containing protein A isoform X3

    3. XM_054324559.1 → XP_054180534.1  ubiquitin-associated and SH3 domain-containing protein A isoform X2

    4. XM_054324563.1 → XP_054180538.1  ubiquitin-associated and SH3 domain-containing protein A isoform X6

    5. XM_054324561.1 → XP_054180536.1  ubiquitin-associated and SH3 domain-containing protein A isoform X4

    6. XM_054324564.1 → XP_054180539.1  ubiquitin-associated and SH3 domain-containing protein A isoform X6

    7. XM_054324566.1 → XP_054180541.1  ubiquitin-associated and SH3 domain-containing protein A isoform X8

    8. XM_054324565.1 → XP_054180540.1  ubiquitin-associated and SH3 domain-containing protein A isoform X7

    9. XM_054324567.1 → XP_054180542.1  ubiquitin-associated and SH3 domain-containing protein A isoform X8

    10. XM_054324562.1 → XP_054180537.1  ubiquitin-associated and SH3 domain-containing protein A isoform X5

    11. XM_054324568.1 → XP_054180543.1  ubiquitin-associated and SH3 domain-containing protein A isoform X9

    RNA

    1. XR_008485337.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P57075.1 GenPept UniProtKB/Swiss-Prot:P57075

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