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SNRPN small nuclear ribonucleoprotein polypeptide N [ Homo sapiens (human) ]

Gene ID: 6638, updated on 12-Oct-2019

Summary

Official Symbol
SNRPNprovided by HGNC
Official Full Name
small nuclear ribonucleoprotein polypeptide Nprovided by HGNC
Primary source
HGNC:HGNC:11164
See related
Ensembl:ENSG00000128739 MIM:182279
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
SMN; PWCR; SM-D; sm-N; RT-LI; HCERN3; SNRNP-N; SNURF-SNRPN
Summary
This gene is located within the Prader-Willi Syndrome critical region on chromosome 15 and is imprinted and expressed from the paternal allele. It encodes a component of the small nuclear ribonucleoprotein complex, which functions in pre-mRNA processing and may contribute to tissue-specific alternative splicing. Alternative promoter use and alternative splicing result in a multitude of transcript variants encoding the same protein. Transcript variants that initiate at the CpG island-associated imprinting center may be bicistronic and also encode the SNRPN upstream reading frame protein (SNURF) from an upstream open reading frame. In addition, long spliced transcripts for small nucleolar RNA host gene 14 (SNHG14) may originate from the promoters at this locus and share exons with this gene. Alterations in this region are associated with parental imprint switch failure, which may cause Angelman syndrome or Prader-Willi syndrome. [provided by RefSeq, Mar 2017]
Orthologs

Genomic context

See SNRPN in Genome Data Viewer
Location:
15q11.2
Exon count:
20
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (24823608..24978723)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (25068794..25223730)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene nuclear pore associated protein 1 Neighboring gene Sharpr-MPRA regulatory region 9168 Neighboring gene Sharpr-MPRA regulatory region 849 Neighboring gene small nucleolar RNA host gene 14 Neighboring gene ribosomal protein S27 pseudogene 2 Neighboring gene ribosomal protein L5 pseudogene 1 Neighboring gene small nucleolar RNA, C/D box 107 Neighboring gene SNRPN upstream reading frame Neighboring gene small nucleolar RNA, C/D box 64 Neighboring gene Prader Willi/Angelman region RNA, SNRPN neighbor Neighboring gene Prader Willi/Angelman region RNA 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
Autistic disorder of childhood onset
MedGen: C0004352 OMIM: 209850 GeneReviews: Not available
Compare labs
Prader-Willi syndrome
MedGen: C0032897 OMIM: 176270 GeneReviews: Prader-Willi Syndrome
Compare labs

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated (2012-10-26)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated (2012-10-26)

ClinGen Genome Curation Page

NHGRI GWAS Catalog

Description
Framingham Heart Study genome-wide association: results for pulmonary function measures.
NHGRI GWA Catalog
Genome-wide association study of chronic periodontitis in a general German population.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr is identified to have a physical interaction with small nuclear ribonucleoprotein polypeptide N (SNRPN) 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

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...
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • 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

Clone Names

  • FLJ33569, FLJ36996, FLJ39265, MGC29886, DKFZp762N022, DKFZp686C0927, DKFZp761I1912, DKFZp686M12165

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA splicing TAS
Traceable Author Statement
more info
PubMed 
mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
response to hormone IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
U1 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U2 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U2-type prespliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U4 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U4/U6 x U5 tri-snRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U5 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
small nuclear ribonucleoprotein complex TAS
Traceable Author Statement
more info
PubMed 
spliceosomal complex TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
small nuclear ribonucleoprotein-associated protein N
Names
SM protein N
sm protein D
tissue-specific splicing protein

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_012958.1 RefSeqGene

    Range
    4962..160077
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
  2. NG_002690.1 

    Range
    42698..197814
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001349454.1NP_001336383.1  small nuclear ribonucleoprotein-associated protein N

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) represents use of an alternate promoter compared to variant 1.
    Source sequence(s)
    AC090983, AC124312, BC035280
    Consensus CDS
    CCDS10017.1
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  2. NM_001349455.1NP_001336384.1  small nuclear ribonucleoprotein-associated protein N

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) represents use of an alternate upstream promoter compared to variant 1.
    Source sequence(s)
    AC090602, AC090983, AC124312
    Consensus CDS
    CCDS10017.1
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  3. NM_001349456.1NP_001336385.1  small nuclear ribonucleoprotein-associated protein N

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) represents use of an alternate upstream promoter compared to variant 1.
    Source sequence(s)
    AC090602, AC090983, AC124312
    Consensus CDS
    CCDS10017.1
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  4. NM_001349457.1NP_001336386.1  small nuclear ribonucleoprotein-associated protein N

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) represents use of an alternate upstream promoter compared to variant 1.
    Source sequence(s)
    AC090602, AC090983, AC124312
    Consensus CDS
    CCDS10017.1
    Related
    ENSP00000494831.1, ENST00000645002.1
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  5. NM_001349458.1NP_001336387.1  small nuclear ribonucleoprotein-associated protein N

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) represents use of an alternate upstream promoter compared to variant 1.
    Source sequence(s)
    AC090602, AC090983, AC124312
    Consensus CDS
    CCDS10017.1
    Related
    ENSP00000495345.1, ENST00000642807.1
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  6. NM_001349459.1NP_001336388.1  small nuclear ribonucleoprotein-associated protein N

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11) represents use of an alternate upstream promoter compared to variant 1.
    Source sequence(s)
    AC090602, AC090983, AC124312
    Consensus CDS
    CCDS10017.1
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  7. NM_001349460.1NP_001336389.1  small nuclear ribonucleoprotein-associated protein N

    Status: REVIEWED

    Description
    Transcript Variant: This variant (12) represents use of an alternate upstream promoter compared to variant 1.
    Source sequence(s)
    AC090602, AC090983, AC124312
    Consensus CDS
    CCDS10017.1
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  8. NM_001349461.1NP_001336390.1  small nuclear ribonucleoprotein-associated protein N

    Status: REVIEWED

    Description
    Transcript Variant: This variant (13) represents use of an alternate promoter compared to variant 1.
    Source sequence(s)
    AC090602, AC090983, AC124312
    Consensus CDS
    CCDS10017.1
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  9. NM_001349462.1NP_001336391.1  small nuclear ribonucleoprotein-associated protein N

    Status: REVIEWED

    Description
    Transcript Variant: This variant (14) represents use of an alternate promoter compared to variant 1.
    Source sequence(s)
    AC090602, AC090983, AC124312
    Consensus CDS
    CCDS10017.1
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  10. NM_001349463.1NP_001336392.1  small nuclear ribonucleoprotein-associated protein N

    Status: REVIEWED

    Description
    Transcript Variant: This variant (15) represents use of the same promoter as variant 1.
    Source sequence(s)
    AC090602, AC124312
    Consensus CDS
    CCDS10017.1
    Related
    ENSP00000452342.2, ENST00000554227.6
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  11. NM_001349464.1NP_001336393.1  small nuclear ribonucleoprotein-associated protein N

    Status: REVIEWED

    Description
    Transcript Variant: This variant (16) represents use of the same promoter as variant 1.
    Source sequence(s)
    AC090602, AC124312
    Consensus CDS
    CCDS10017.1
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  12. NM_001349465.1NP_001336394.1  small nuclear ribonucleoprotein-associated protein N

    Status: REVIEWED

    Description
    Transcript Variant: This variant (17) represents use of the same promoter as variant 1.
    Source sequence(s)
    AC090602, AC124312
    Consensus CDS
    CCDS10017.1
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  13. NM_003097.5NP_003088.1  small nuclear ribonucleoprotein-associated protein N

    See identical proteins and their annotated locations for NP_003088.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is the predominant splice variant and initiates at the imprinting center. This splice variant is bicistronic and can also encode the SNURF protein from an upstream open reading frame.
    Source sequence(s)
    AC090602, AC124312, U41303
    Consensus CDS
    CCDS10017.1
    UniProtKB/Swiss-Prot
    P63162
    UniProtKB/TrEMBL
    X5DP00
    Related
    ENSP00000375105.4, ENST00000390687.8
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  14. NM_022805.4NP_073716.1  small nuclear ribonucleoprotein-associated protein N

    See identical proteins and their annotated locations for NP_073716.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents use of an alternate promoter compared to variant 1.
    Source sequence(s)
    AC090602, AC090983, AC124312, L80004
    Consensus CDS
    CCDS10017.1
    UniProtKB/Swiss-Prot
    P63162
    UniProtKB/TrEMBL
    X5DP00
    Related
    ENSP00000382969.1, ENST00000400097.5
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  15. NM_022806.4NP_073717.1  small nuclear ribonucleoprotein-associated protein N

    See identical proteins and their annotated locations for NP_073717.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents use of an alternate upstream promoter compared to variant 1.
    Source sequence(s)
    AC090983, AC124312, DA131564, L80004
    Consensus CDS
    CCDS10017.1
    UniProtKB/Swiss-Prot
    P63162
    UniProtKB/TrEMBL
    X5DP00
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  16. NM_022807.4NP_073718.1  small nuclear ribonucleoprotein-associated protein N

    See identical proteins and their annotated locations for NP_073718.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) represents use of an alternate upstream promoter compared to variant 1.
    Source sequence(s)
    AC090602, AC090983, AC124312, L80005
    Consensus CDS
    CCDS10017.1
    UniProtKB/Swiss-Prot
    P63162
    UniProtKB/TrEMBL
    X5DP00
    Related
    ENSP00000382972.1, ENST00000400100.5
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B
  17. NM_022808.4NP_073719.1  small nuclear ribonucleoprotein-associated protein N

    See identical proteins and their annotated locations for NP_073719.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) represents use of an alternate upstream promoter compared to variant 1.
    Source sequence(s)
    AC090602, AC090983, AC124312, L80004, L80005
    Consensus CDS
    CCDS10017.1
    UniProtKB/Swiss-Prot
    P63162
    UniProtKB/TrEMBL
    X5DP00
    Conserved Domains (1) summary
    cd01717
    Location:583
    Sm_B; Sm protein B

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    24823608..24978723
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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