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SSB small RNA binding exonuclease protection factor La [ Homo sapiens (human) ]

Gene ID: 6741, updated on 3-Nov-2024

Summary

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Official Symbol
SSBprovided by HGNC
Official Full Name
small RNA binding exonuclease protection factor Laprovided by HGNC
Primary source
HGNC:HGNC:11316
See related
Ensembl:ENSG00000138385 MIM:109090; AllianceGenome:HGNC:11316
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
La; LARP3; La/SSB
Summary
The protein encoded by this gene is involved in diverse aspects of RNA metabolism, including binding and protecting poly(U) termini of nascent RNA polymerase III transcripts from exonuclease digestion, processing 5' and 3' ends of pre-tRNA precursors, acting as an RNA chaperone, and binding viral RNAs associated with hepatitis C virus. Autoantibodies reacting with this protein are found in the sera of patients with Sjogren syndrome and systemic lupus erythematosus. Alternative promoter usage results in two different transcript variants which encode the same protein. [provided by RefSeq, Jun 2014]
Expression
Ubiquitous expression in fat (RPKM 51.7), thyroid (RPKM 36.0) and 25 other tissues See more
Orthologs
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Genomic context

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See SSB in Genome Data Viewer
Location:
2q31.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (169798871..169812064)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (170276405..170289608)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (170655381..170668574)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:170646034-170646713 Neighboring gene uncharacterized LOC124907905 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:170655164-170655664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12086 Neighboring gene cytochrome b5 type A pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:170681961-170682164 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12087 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:170685725-170686226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:170686227-170686726 Neighboring gene methyltransferase 5, N6-adenosine Neighboring gene small nucleolar RNA, C/D box 3K Neighboring gene ReSE screen-validated silencer GRCh37_chr2:170696663-170696887 Neighboring gene ubiquitin protein ligase E3 component n-recognin 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:170809766-170810965 Neighboring gene Sharpr-MPRA regulatory region 15130 Neighboring gene VISTA enhancer hs1867 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:170934286-170935065 Neighboring gene NSA2 pseudogene 5

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 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LARP3, LARP7, and MePCE are involved in the early stage of human telomerase RNA biogenesis.
    Title: LARP3, LARP7, and MePCE are involved in the early stage of human telomerase RNA biogenesis.
  2. NMR Analysis Suggests Synergy between the RRM2 and the Carboxy-Terminal Segment of Human La Protein in the Recognition and Interaction with HCV IRES.
    Title: NMR Analysis Suggests Synergy between the RRM2 and the Carboxy-Terminal Segment of Human La Protein in the Recognition and Interaction with HCV IRES.
  3. Upregulated SSB Is Involved in Hepatocellular Carcinoma Progression and Metastasis through the Epithelial-Mesenchymal Transition, Antiapoptosis, and Altered ROS Level Pathway.
    Title: Upregulated SSB Is Involved in Hepatocellular Carcinoma Progression and Metastasis through the Epithelial-Mesenchymal Transition, Antiapoptosis, and Altered ROS Level Pathway.
  4. The RNA-binding protein La/SSB associates with radiation-induced DNA double-strand breaks in lung cancer cell lines.
    Title: The RNA-binding protein La/SSB associates with radiation-induced DNA double-strand breaks in lung cancer cell lines.
  5. RNA-binding proteins La and HuR cooperatively modulate translation repression of PDCD4 mRNA.
    Title: RNA-binding proteins La and HuR cooperatively modulate translation repression of PDCD4 mRNA.
  6. Sjogren Syndrome antigen B regulates LIN28-let-7 axis in Caenorhabditis elegans and human.
    Title: Sjögren Syndrome antigen B regulates LIN28-let-7 axis in Caenorhabditis elegans and human.
  7. Functional and Structural Aspects of La Protein Overexpression in Lung Cancer.
    Title: Functional and Structural Aspects of La Protein Overexpression in Lung Cancer.
  8. Data is consistent with human La functioning in translation through contacts to the poly(A) tail.
    Title: Human La binds mRNAs through contacts to the poly(A) tail.
  9. Sumoylation of La protein promotes cell proliferation by averting ubiquitination-mediated degradation of the STAT3 protein.
    Title: SUMO Modification of the RNA-Binding Protein La Regulates Cell Proliferation and STAT3 Protein Stability.
  10. A cytoplasmic isoform of La protein as well as LARPs 6, 4, and 1 function in mRNA metabolism and translation in distinct but similar ways, sometimes with the poly(A)-binding protein, and in some cases by direct binding to poly(A)-RNA.
    Title: The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives.
Submit: New GeneRIF Correction See all GeneRIFs (78)

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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of Sjogren syndrome antigen B (SSB) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev is identified to have a physical interaction with Sjogren syndrome antigen B ( SSB) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
rev HIV-1 Rev interacting protein, Sjogren syndrome antigen B (SSB), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with SSB is increased by RRE PubMed
Tat tat The La autoantigen binds to HIV-1 TAR RNA and alleviates translational repression by the HIV-1 leader RNA, suggesting a possible involvement of the La autoantigen in HIV-1 gene expression and Tat transactivation PubMed
Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of Sjogren syndrome antigen B (SSB, autoantigen La) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed
retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human Sjogren syndrome antigen B (SSB; autoantigen La) at amino acid residues 24-25 by the HIV-1 protease 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 RNA binding HDA PubMed 
enables RNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables poly(U) RNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables poly(U) RNA binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific mRNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables tRNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in IRES-dependent viral translational initiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in histone mRNA metabolic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in nuclear histone mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein localization to cytoplasmic stress granule IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in tRNA 3'-end processing IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in tRNA 5'-leader removal IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in tRNA export from nucleus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in tRNA modification TAS
Traceable Author Statement
more info
 PubMed 
involved_in tRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in chromosome, telomeric region HDA PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasmic stress granule IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of ribonucleoprotein complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
lupus La protein
Names
La ribonucleoprotein domain family, member 3
SS-B
SS-B/La protein
Sjogren syndrome antigen B
autoantigen La
la autoantigen
lupus La antigen
sjoegren syndrome type B antigen

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_030640.1 RefSeqGene

    Range
    5060..18253
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001294145.2 → NP_001281074.1  lupus La protein

    See identical proteins and their annotated locations for NP_001281074.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 5' UTR exon and encodes the same protein, compared to variant 1.
    Source sequence(s)
    BC001289, X69804
    Consensus CDS
    CCDS2237.1
    UniProtKB/Swiss-Prot
    P05455, Q15367, Q53XJ4
    UniProtKB/TrEMBL
    B5BUB5
    Related
    ENSP00000386636.1, ENST00000409333.1
    Conserved Domains (3) summary
    cd08028
    Location:10 → 91
    LARP_3; La RNA-binding domain of La-related protein 3
    cd12291
    Location:112 → 183
    RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
    pfam08777
    Location:231 → 334
    RRM_3; RNA binding motif

  2. NM_003142.5 → NP_003133.1  lupus La protein

    See identical proteins and their annotated locations for NP_003133.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) and variant 2 encode the same protein.
    Source sequence(s)
    BC001289, CD676196
    Consensus CDS
    CCDS2237.1
    UniProtKB/Swiss-Prot
    P05455, Q15367, Q53XJ4
    UniProtKB/TrEMBL
    B5BUB5
    Related
    ENSP00000260956.4, ENST00000260956.9
    Conserved Domains (3) summary
    cd08028
    Location:10 → 91
    LARP_3; La RNA-binding domain of La-related protein 3
    cd12291
    Location:112 → 183
    RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
    pfam08777
    Location:231 → 334
    RRM_3; RNA binding motif

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    169798871..169812064
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    170276405..170289608
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P05455.2 GenPept UniProtKB/Swiss-Prot:P05455

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
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