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    SMU1 SMU1 DNA replication regulator and spliceosomal factor [ Homo sapiens (human) ]

    Gene ID: 55234, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SMU1provided by HGNC
    Official Full Name
    SMU1 DNA replication regulator and spliceosomal factorprovided by HGNC
    Primary source
    HGNC:HGNC:18247
    See related
    Ensembl:ENSG00000122692 MIM:617811; AllianceGenome:HGNC:18247
    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
    BWD; SMU-1; fSAP57
    Summary
    Involved in mRNA splicing, via spliceosome. Located in nucleus. Part of U2-type precatalytic spliceosome. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in brain (RPKM 7.9), thyroid (RPKM 7.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMU1 in Genome Data Viewer
    Location:
    9p21.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (33041765..33076674, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (33058326..33097983, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (33041763..33076672, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene aprataxin Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:33024111-33024706 Neighboring gene Sharpr-MPRA regulatory region 3987 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:33025301-33025895 Neighboring gene L antigen family member 3 pseudogene 1 Neighboring gene DnaJ heat shock protein family (Hsp40) member A1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:33043981-33044482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:33111589-33112188 Neighboring gene beta-1,4-galactosyltransferase 1 Neighboring gene microRNA 12117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28273 Neighboring gene uncharacterized LOC124902141

    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. SMU1 Knockdown Suppresses Gastric Carcinoma Growth, Migration, and Invasion and Modulates the Cell Cycle. Qian M, et al. Cancer Control, 2024 Jan-Dec. PMID 39236066, Free PMC Article
    2. Loss of Smu1 function de-represses DNA replication and over-activates ATR-dependent replication checkpoint. Ren L, et al. Biochem Biophys Res Commun, 2013 Jun 28. PMID 23727573
    3. Smu1 and RED are required for activation of spliceosomal B complexes assembled on short introns. Keiper S, et al. Nat Commun, 2019 Aug 13. PMID 31409787, Free PMC Article
    4. Destabilization of the human RED-SMU1 splicing complex as a basis for host-directed antiinfluenza strategy. Ashraf U, et al. Proc Natl Acad Sci U S A, 2019 May 28. PMID 31076555, Free PMC Article
    5. Cloning and molecular characterization of a novel gene encoding a WD-repeat protein expressed in restricted areas of adult rat brain. Di Benedetto AJ, et al. Gene, 2001 Jun 13. PMID 11410362

    See all (115) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SMU1 Knockdown Suppresses Gastric Carcinoma Growth, Migration, and Invasion and Modulates the Cell Cycle.
      Title: SMU1 Knockdown Suppresses Gastric Carcinoma Growth, Migration, and Invasion and Modulates the Cell Cycle.
    2. Investigated and identified antiviral agents targeting the assembly of the human RED-SMU1 splicing complex, and results demonstrate possibility of RED-SMU1 destabilizing molecules to be used in antiviral therapy.
      Title: Destabilization of the human RED-SMU1 splicing complex as a basis for host-directed antiinfluenza strategy.
    3. Smu1 and RED function both as alternative splicing regulators and as general splicing factors and are required predominantly for efficient splicing of short introns.
      Title: Smu1 and RED are required for activation of spliceosomal B complexes assembled on short introns.
    4. Results unveil an important role of CRL7(SMU1) E3 ligase in promoting H2B ubiquitylation for maintenance of sister chromatid cohesion during mitosis.
      Title: CRL7(SMU1) E3 ligase complex-driven H2B ubiquitylation functions in sister chromatid cohesion by regulating SMC1 expression.
    5. Data suggest that two human spliceosomal factors, SMU1 and RED, are recruited to control expression and alternative splicing of viral exportins via PB2 (polymerase PB2) of influenza A virus (H3N2) and are required for efficient viral multiplication.
      Title: Recruitment of RED-SMU1 complex by Influenza A Virus RNA polymerase to control Viral mRNA splicing.
    6. Data suggest that Smu1 participates in the protection of genomic integrity by negatively regulating the process of DNA synthesis.
      Title: Loss of Smu1 function de-represses DNA replication and over-activates ATR-dependent replication checkpoint.
    7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans) (SMU1) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev is identified to have a physical interaction with suppressor of mec-8 and unc-52 homolog (SMU-1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10805, FLJ10870, FLJ11970, MGC117363, DKFZp761L0916

    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 RNA splicing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of alternative mRNA splicing, via spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of U2-type precatalytic spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear speck ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of precatalytic spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    WD40 repeat-containing protein SMU1
    Names
    DNA replication regulator and spliceosomal factor
    brain-enriched WD-repeat protein
    functional spliceosome-associated protein 57
    smu-1 suppressor of mec-8 and unc-52 homolog
    smu-1 suppressor of mec-8 and unc-52 protein homolog

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_018225.3 → NP_060695.2  WD40 repeat-containing protein SMU1

      See identical proteins and their annotated locations for NP_060695.2

      Status: VALIDATED

      Source sequence(s)
      AK001667, AL162590
      Consensus CDS
      CCDS6534.1
      UniProtKB/Swiss-Prot
      B4E3L0, Q2TAY7, Q9BU59, Q9HA96, Q9NVD1
      UniProtKB/TrEMBL
      A0MNN4, A8MXW4
      Related
      ENSP00000380336.3, ENST00000397149.4
      Conserved Domains (5) summary
      smart00668
      Location:40 → 90
      CTLH; C-terminal to LisH motif
      COG4598
      Location:102 → 218
      HisP; ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]
      cd00200
      Location:205 → 512
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      sd00039
      Location:219 → 262
      7WD40; WD40 repeat [structural motif]
      pfam17814
      Location:7 → 36
      LisH_TPL; LisH-like dimerisation domain

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      33041765..33076674 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005251503.6 → XP_005251560.1  WD40 repeat-containing protein SMU1 isoform X1

      See identical proteins and their annotated locations for XP_005251560.1

      Conserved Domains (5) summary
      smart00667
      Location:5 → 38
      LisH; Lissencephaly type-1-like homology motif
      smart00668
      Location:40 → 81
      CTLH; C-terminal to LisH motif
      COG2319
      Location:161 → 462
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:154 → 461
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
      sd00039
      Location:168 → 211
      7WD40; WD40 repeat [structural motif]

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      33058326..33097983 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363216.1 → XP_054219191.1  WD40 repeat-containing protein SMU1 isoform X2

      UniProtKB/Swiss-Prot
      B4E3L0, Q2TAY7, Q9BU59, Q9HA96, Q9NVD1
      UniProtKB/TrEMBL
      A0MNN4, A8MXW4

    2. XM_054363217.1 → XP_054219192.1  WD40 repeat-containing protein SMU1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q2TAY7.2 GenPept UniProtKB/Swiss-Prot:Q2TAY7

    Gene LinkOut

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

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