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

Gene ID: 10285, updated on 7-Oct-2019

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
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

Genomic context

See SMNDC1 in Genome Data Viewer
Location:
10q25.2
Exon count:
7
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (110290730..110304969, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (112052798..112064707, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378479 Neighboring gene uncharacterized LOC105378480 Neighboring gene MAX interactor 1, dimerization protein Neighboring gene uncharacterized LOC105378482 Neighboring gene high mobility group box 3 pseudogene 5

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Spinal muscular atrophy
MedGen: C0026847 GeneReviews: Spinal Muscular Atrophy
Compare labs

NHGRI 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.
NHGRI GWA Catalog

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA splicing, via transesterification reactions TAS
Traceable Author Statement
more info
PubMed 
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
Cajal body IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nuclear speck IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus TAS
Traceable Author Statement
more info
PubMed 
spliceosomal complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

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)

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.

Genomic

  1. NG_008284.1 RefSeqGene

    Range
    5001..16910
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005871.4NP_005862.1  survival of motor neuron-related-splicing factor 30

    See identical proteins and their annotated locations for NP_005862.1

    Status: REVIEWED

    Source sequence(s)
    AL360182, BC011234, BQ694303
    Consensus CDS
    CCDS7565.1
    UniProtKB/Swiss-Prot
    O75940
    Related
    ENSP00000358616.4, ENST00000369603.10
    Conserved Domains (1) summary
    pfam06003
    Location:69124
    SMN; Survival motor neuron protein (SMN)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    110290730..110304969 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005269382.3XP_005269439.1  survival of motor neuron-related-splicing factor 30 isoform X1

    Conserved Domains (1) summary
    cd04508
    Location:3785
    TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
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