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

Gene ID: 55234, updated on 7-Apr-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, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 7.9), thyroid (RPKM 7.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
9p21.1
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (33041765..33076674, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (33058326..33097983, complement)
105.20220307 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: 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. 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
  2. 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
  3. 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
  4. Recruitment of RED-SMU1 complex by Influenza A Virus RNA polymerase to control Viral mRNA splicing. Fournier G, et al. PLoS Pathog, 2014 Jun. PMID 24945353, 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 (97) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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)

Genotypes

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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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_2023_10

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

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