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    SNRPA small nuclear ribonucleoprotein polypeptide A [ Homo sapiens (human) ]

    Gene ID: 6626, updated on 7-Apr-2024

    Summary

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    Official Symbol
    SNRPAprovided by HGNC
    Official Full Name
    small nuclear ribonucleoprotein polypeptide Aprovided by HGNC
    Primary source
    HGNC:HGNC:11151
    See related
    Ensembl:ENSG00000077312 MIM:182285; AllianceGenome:HGNC:11151
    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
    U1A; Mud1; U1-A
    Summary
    The protein encoded by this gene associates with stem loop II of the U1 small nuclear ribonucleoprotein, which binds the 5' splice site of precursor mRNAs and is required for splicing. The encoded protein autoregulates itself by polyadenylation inhibition of its own pre-mRNA via dimerization and has been implicated in the coupling of splicing and polyadenylation. [provided by RefSeq, Oct 2010]
    Expression
    Ubiquitous expression in spleen (RPKM 22.2), lymph node (RPKM 20.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    19q13.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (40751203..40765389)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (43571894..43586079)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (41257108..41271294)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10645 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:41224841-41225542 Neighboring gene inositol-trisphosphate 3-kinase C Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41249947-41250913 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41250914-41251879 Neighboring gene actin maturation protease Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41255833-41256458 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14665 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41257087-41257714 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41257715-41258342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14666 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10647 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14667 Neighboring gene MIA-RAB4B readthrough (NMD candidate) Neighboring gene RAB4B-EGLN2 readthrough (NMD candidate) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41285223-41285754 Neighboring gene MIA SH3 domain containing Neighboring gene RAB4B, member RAS oncogene family

    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. Exome sequencing reveals three homozygous missense variants in SNRPA in two sisters with syndromic intellectual disability. Rangel-Sosa MM, et al. Clin Genet, 2018 Jun. PMID 29437235
    2. Multistep kinetics of the U1A-SL2 RNA complex dissociation. Anunciado D, et al. J Mol Biol, 2011 May 20. PMID 21419778
    3. U1A protein-stem loop 2 RNA recognition: prediction of structural differences from protein mutations. Kormos BL, et al. Biopolymers, 2011 Sep. PMID 21384338, Free PMC Article
    4. A bipartite U1 site represses U1A expression by synergizing with PIE to inhibit nuclear polyadenylation. Guan F, et al. RNA, 2007 Dec. PMID 17942741, Free PMC Article
    5. 13C NMR relaxation studies of RNA base and ribose nuclei reveal a complex pattern of motions in the RNA binding site for human U1A protein. Shajani Z, et al. J Mol Biol, 2005 Jun 17. PMID 15890361

    See all (155) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Circ_0009910 Serves as miR-361-3p Sponge to Promote the Proliferation, Metastasis, and Glycolysis of Gastric Cancer via Regulating SNRPA.
      Title: Circ_0009910 Serves as miR-361-3p Sponge to Promote the Proliferation, Metastasis, and Glycolysis of Gastric Cancer via Regulating SNRPA.
    2. The Small Nuclear Ribonucleoprotein Polypeptide A (SNRPA) binds to the G-quadruplex of the BAG-1 5'UTR.
      Title: The Small Nuclear Ribonucleoprotein Polypeptide A (SNRPA) binds to the G-quadruplex of the BAG-1 5'UTR.
    3. Screen using siRNA revealed depletion of U1 snRNP components SNRPA, SNRNP70 or SNRPD2 caused significant cytoplasmic localization of MEG3 reporter transcripts.
      Title: Nuclear retention element recruits U1 snRNP components to restrain spliced lncRNAs in the nucleus.
    4. the previously unreported concurrence of intellectual disability, short stature, poor speech, and minor craniofacial and hand anomalies in 2 female siblings with 3 homozygous missense variants in SNRPA, is reported.
      Title: Exome sequencing reveals three homozygous missense variants in SNRPA in two sisters with syndromic intellectual disability.
    5. SNRPA may contribute to GC progression via NGF and could be a prognostic biomarker for GC.
      Title: SNRPA enhances tumour cell growth in gastric cancer through modulating NGF expression.
    6. p65 activation triggered by TCR signaling could promote SNRPA transcription and 3' UTR shortening of STAT5B. Thus we propose that the alternative polyadenylation switching of STAT5B induced by TCR activation is mediated by SNRPA.
      Title: Small Nuclear Ribonucleoprotein Polypeptide A-Mediated Alternative Polyadenylation of STAT5B during Th1 Cell Differentiation.
    7. a new mechanism for regulating SMN levels and provides new insight into the roles of U1A in 3' processing of mRNAs.
      Title: U1A regulates 3' processing of the survival motor neuron mRNA.
    8. An analysis of the kinetic data suggests three phases of U1A-SL2 RNA complex dissociation with time scales of approximately 100 mus, approximately 50 ms, and approximately 2 s. We propose that the first step of dissociation is a fast rearrangement of the complex to form a loosely bound complex.
      Title: Multistep kinetics of the U1A-SL2 RNA complex dissociation.
    9. structural analysis of U1A protein-stem loop 2 RNA recognition
      Title: U1A protein-stem loop 2 RNA recognition: prediction of structural differences from protein mutations.
    10. study shows that the yellow fever virus (YFV) NS5 protein is able to interact with U1A, a protein involved in splicing and polyadenylation; a region between amino acids 368 and 448 was identified as the site of interaction of the NS5 protein with U1A
      Title: The small nuclear ribonucleoprotein U1A interacts with NS5 from yellow fever virus.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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 small nuclear ribonucleoprotein polypeptide A (SNRPA) 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
    Nef nef Expression of HIV-1 Nef in human T cells upregulates U1 SNRNP, a factor that positively regulates HIV-1 PubMed
    Tat tat Small nuclear ribonucleoprotein polypeptide A (SNRPA) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS PubMed
    tat Expression of HIV-1 Tat downregulates the abundance of small nuclear ribonucleoprotein polypeptide A (SNRPA) in the nucleoli of Jurkat T-cells 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 DNA binding EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables RNA binding EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables RNA binding HDA PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables U1 snRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables U1 snRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables U1 snRNP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of U1 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U1 snRNP IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U1 snRNP IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of U4/U6 x U5 tri-snRNP complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of spliceosomal complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of spliceosomal complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    U1 small nuclear ribonucleoprotein A
    Names
    U1 small nuclear RNP-specific A
    U1 snRNP A
    U1 snRNP-specific protein A

    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_004596.5 → NP_004587.1  U1 small nuclear ribonucleoprotein A

      See identical proteins and their annotated locations for NP_004587.1

      Status: REVIEWED

      Source sequence(s)
      AC020945, BC000405
      Consensus CDS
      CCDS12565.1
      UniProtKB/Swiss-Prot
      P09012
      UniProtKB/TrEMBL
      B2R802
      Related
      ENSP00000243563.2, ENST00000243563.8
      Conserved Domains (2) summary
      cd12477
      Location:7 → 95
      RRM1_U1A; RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)
      cd12480
      Location:197 → 282
      RRM2_U1A; RNA recognition motif 2 (RRM2) found in vertebrate U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A)

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      40751203..40765389
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      43571894..43586079
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P09012.3 GenPept UniProtKB/Swiss-Prot:P09012

    Gene LinkOut

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