SMNDC1 survival motor neuron domain containing 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMNDC1provided by HGNC
Official Full Name: survival motor neuron domain containing 1provided by HGNC
Primary source: HGNC:HGNC:16900
See related: Ensembl:ENSG00000119953 MIM:603519; AllianceGenome:HGNC:16900
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: SMNR; SPF30; TDRD16C
Summary: This gene is a paralog of SMN1 gene, which encodes the survival motor neuron protein, mutations in which are cause of autosomal recessive proximal spinal muscular atrophy. The protein encoded by this gene is a nuclear protein that has been identified as a constituent of the spliceosome complex. This gene is differentially expressed, with abundant levels in skeletal muscle, and may share similar cellular function as the SMN1 gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in bone marrow (RPKM 20.9), lymph node (RPKM 13.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q25.2

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (110290730..110304920, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (111174603..111188795, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (112050488..112064678, complement)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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?

An autoregulatory poison exon in Smndc1 is conserved across kingdoms and influences organism growth.
Title: An autoregulatory poison exon in Smndc1 is conserved across kingdoms and influences organism growth.
SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression.
Title: SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression.
Interactome analysis of the Tudor domain-containing protein SPF30 which associates with the MTR4-exosome RNA-decay machinery under the regulation of AAA-ATPase NVL2.
Title: Interactome analysis of the Tudor domain-containing protein SPF30 which associates with the MTR4-exosome RNA-decay machinery under the regulation of AAA-ATPase NVL2.
Low SMNDC1 expression is associated with lung cancer.
Title: RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons.
The results show that SMNDC1 mRNA 5'-UTR forms an intramolecular, parallel G quadruplex structure comprised of three G quartet planes, which is bound specifically by FMRP both in vitro and in mouse brain lysates.
Title: Fragile X mental retardation protein recognizes a G quadruplex structure within the survival motor neuron domain containing 1 mRNA 5'-UTR.
The binding specificity and affinity of the Tudor domains of TDRD3, SMN and SPF30 proteins were characterized quantitatively.
Title: Crystal structure of TDRD3 and methyl-arginine binding characterization of TDRD3, SMN and SPF30.
The structures of SMN and SPF30 Tudor domains bound to symmetric and asymmetric dimethylated arginine (DMA) are presented.
Title: Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins.
Observational study of gene-disease association. (HuGE Navigator)
Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
U2AF35 and hPrp3 interactions with SPF30 can occur simultaneously, thereby potentially linking 3' splice site recognition with tri-small nuclear ribonucleoprotein addition
Title: Splicing factor SPF30 bridges an interaction between the prespliceosome protein U2AF35 and tri-small nuclear ribonucleoprotein protein hPrp3.

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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

Associated conditions

Description	Tests
Spinal muscular atrophy MedGen: C0026847 GeneReviews: Spinal Muscular Atrophy	not available

EBI GWAS Catalog

Description
Genome-wide association study of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA splicing, via transesterification reactions	TAS Traceable Author Statement more info	PubMed
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Cajal body	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of spliceosomal complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: survival of motor neuron-related-splicing factor 30

Names: 30 kDa splicing factor SMNrp; SMN-related protein; splicing factor 30, survival of motor neuron-related; survival motor neuron domain-containing protein 1; tudor domain containing 16C

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.