Format

Send to:

Choose Destination

SMN2 survival of motor neuron 2, centromeric [ Homo sapiens (human) ]

Gene ID: 6607, updated on 6-Sep-2021

Summary

Official Symbol
SMN2provided by HGNC
Official Full Name
survival of motor neuron 2, centromericprovided by HGNC
Primary source
HGNC:HGNC:11118
See related
Ensembl:ENSG00000205571 MIM:601627
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
SMNC; BCD541; GEMIN1; TDRD16B; C-BCD541
Summary
This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and complexity of the sequence have also caused difficulty in determining the organization of this genomic region. The telomeric and centromeric copies of this gene are nearly identical and encode the same protein. While mutations in the telomeric copy are associated with spinal muscular atrophy, mutations in this gene, the centromeric copy, do not lead to disease. This gene may be a modifier of disease caused by mutation in the telomeric copy. The critical sequence difference between the two genes is a single nucleotide in exon 7, which is thought to be an exon splice enhancer. Note that the nine exons of both the telomeric and centromeric copies are designated historically as exon 1, 2a, 2b, and 3-8. It is thought that gene conversion events may involve the two genes, leading to varying copy numbers of each gene. The full length protein encoded by this gene localizes to both the cytoplasm and the nucleus. Within the nucleus, the protein localizes to subnuclear bodies called gems which are found near coiled bodies containing high concentrations of small ribonucleoproteins (snRNPs). This protein forms heteromeric complexes with proteins such as SIP1 and GEMIN4, and also interacts with several proteins known to be involved in the biogenesis of snRNPs, such as hnRNP U protein and the small nucleolar RNA binding protein. Four transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Sep 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 24.2), testis (RPKM 21.9) and 25 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See SMN2 in Genome Data Viewer
Location:
5q13.2
Exon count:
10
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (70049523..70077595)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (69345350..69373422)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369228 Neighboring gene uncharacterized LOC112267941 Neighboring gene cadherin 12 pseudogene 2 Neighboring gene mitochondrial import receptor subunit TOM5 homolog pseudogene Neighboring gene small EDRK-rich factor 1B Neighboring gene NAIP pseudogene 2 Neighboring gene GUSB pseudogene 14 Neighboring gene cadherin 12 pseudogene 3

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC5208, FLJ76644, MGC20996

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA-templated transcription, termination IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in spliceosomal complex assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in spliceosomal complex assembly NAS
Non-traceable Author Statement
more info
PubMed 
involved_in spliceosomal snRNP assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in spliceosomal snRNP assembly IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
is_active_in Cajal body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in Cajal body IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in Gemini of coiled bodies IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in Gemini of coiled bodies IDA
Inferred from Direct Assay
more info
PubMed 
part_of SMN complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of SMN complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of SMN-Sm protein complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in Z disc IEA
Inferred from Electronic Annotation
more info
 
located_in axon IEA
Inferred from Electronic Annotation
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasmic ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in neuron projection IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear body IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in perikaryon IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
survival motor neuron protein
Names
component of gems 1
gemin-1
tudor domain containing 16B

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_008728.1 RefSeqGene

    Range
    5147..33073
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_677

mRNA and Protein(s)

  1. NM_017411.4NP_059107.1  survival motor neuron protein isoform d

    See identical proteins and their annotated locations for NP_059107.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (d) represents the longest transcript and encodes the longest isoform (d).
    Source sequence(s)
    AI312583, BC015308, CN272420
    Consensus CDS
    CCDS4007.1
    UniProtKB/Swiss-Prot
    Q16637
    Related
    ENSP00000370119.4, ENST00000380743.9
    Conserved Domains (1) summary
    pfam06003
    Location:27291
    SMN; Survival motor neuron protein (SMN)
  2. NM_022875.3NP_075013.1  survival motor neuron protein isoform a

    See identical proteins and their annotated locations for NP_075013.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (a) lacks an alternate exon in the 3' CDS compared to variant d. The resulting protein (isoform a) is shorter and has a distinct C-terminus compared to isoform d. This variant is thought to be the predominant transcript produced by this copy of the gene.
    Source sequence(s)
    AA029652, AI312583, BC000908
    Consensus CDS
    CCDS54867.1
    UniProtKB/Swiss-Prot
    Q16637
    Related
    ENSP00000486152.1, ENST00000626847.2
    Conserved Domains (1) summary
    pfam06003
    Location:27278
    SMN; Survival motor neuron protein (SMN)
  3. NM_022876.2NP_075014.1  survival motor neuron protein isoform b

    See identical proteins and their annotated locations for NP_075014.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (b) lacks an alternate in-frame exon in the 3' CDS compared to variant d. The resulting protein (isoform b) is shorter but has the same N- and C- termini compared to isoform d.
    Source sequence(s)
    AC140134, AI312583, BC015308, CN272420
    Consensus CDS
    CCDS4008.1
    UniProtKB/Swiss-Prot
    Q16637
    Related
    ENSP00000370118.4, ENST00000380742.8
    Conserved Domains (1) summary
    pfam06003
    Location:27259
    SMN; Survival motor neuron protein (SMN)
  4. NM_022877.2NP_075015.1  survival motor neuron protein isoform c

    See identical proteins and their annotated locations for NP_075015.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (c) lacks two alternate exons in the 3' CDS compared to variant d. The resulting protein (isoform c) is shorter and has a distinct C-terminus compared to isoform d.
    Source sequence(s)
    AA029652, AC140134, AI312583, BC000908
    UniProtKB/Swiss-Prot
    Q16637
    Conserved Domains (2) summary
    smart00333
    Location:90147
    TUDOR; Tudor domain
    pfam06003
    Location:27246
    SMN; Survival motor neuron protein (SMN)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    70049523..70077595
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011543602.3XP_011541904.1  survival motor neuron protein isoform X5

    See identical proteins and their annotated locations for XP_011541904.1

    Conserved Domains (1) summary
    pfam06003
    Location:27192
    SMN; Survival motor neuron protein (SMN)
  2. XM_011543603.3XP_011541905.1  survival motor neuron protein isoform X6

    See identical proteins and their annotated locations for XP_011541905.1

    Conserved Domains (1) summary
    pfam06003
    Location:27179
    SMN; Survival motor neuron protein (SMN)
  3. XM_011543600.2XP_011541902.1  survival motor neuron protein isoform X3

    See identical proteins and their annotated locations for XP_011541902.1

    UniProtKB/TrEMBL
    B4DP61
    Related
    ENSP00000424282.1, ENST00000511812.5
    Conserved Domains (1) summary
    pfam06003
    Location:27224
    SMN; Survival motor neuron protein (SMN)
  4. XM_011543601.1XP_011541903.1  survival motor neuron protein isoform X4

    See identical proteins and their annotated locations for XP_011541903.1

    Conserved Domains (1) summary
    pfam06003
    Location:27211
    SMN; Survival motor neuron protein (SMN)
  5. XM_011543599.1XP_011541901.1  survival motor neuron protein isoform X1

    See identical proteins and their annotated locations for XP_011541901.1

    UniProtKB/TrEMBL
    E7EQZ4
    Related
    ENSP00000486268.1, ENST00000628696.2
    Conserved Domains (2) summary
    smart00333
    Location:90147
    TUDOR; Tudor domain
    pfam06003
    Location:27278
    SMN; Survival motor neuron protein (SMN)
  6. XM_017009787.1XP_016865276.1  survival motor neuron protein isoform X2

    Related
    ENSP00000492675.1, ENST00000638794.1

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_187651.1 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    274862..302936
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center