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

Summary

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, Nov 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

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_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.

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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

D5S2354 (e-PCR)
- UniSTS:473392

D8S2279 (e-PCR)
- UniSTS:473907

SHGC-68674 (e-PCR)
- UniSTS:100665

G32760 (e-PCR)
- UniSTS:117341

L17709 (e-PCR)
- UniSTS:42599

D1S1423 (e-PCR)
- UniSTS:149619

RH103320 (e-PCR)
- UniSTS:97651

G35510 (e-PCR)
- UniSTS:44150

RH68042 (e-PCR)
- UniSTS:30103

RH48194 (e-PCR)
- UniSTS:63134

A009Q03 (e-PCR)
- UniSTS:61605

D9S1743 (e-PCR)
- UniSTS:82175

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)

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

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

33041765..33076674 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_060933.1 Alternate T2T-CHM13v2.0

Range

33058326..33097983 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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