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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
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Genomic context

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See UBASH3A in Genome Data Viewer
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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