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SELENON selenoprotein N [ Homo sapiens (human) ]

Gene ID: 57190, updated on 23-Nov-2023

Summary

Official Symbol
SELENONprovided by HGNC
Official Full Name
selenoprotein Nprovided by HGNC
Primary source
HGNC:HGNC:15999
See related
Ensembl:ENSG00000162430 MIM:606210; AllianceGenome:HGNC:15999
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
RSS; CFTD; SELN; CMYP3; MDRS1; RSMD1; SEPN1
Summary
This gene encodes a glycoprotein that is localized in the endoplasmic reticulum. It plays an important role in cell protection against oxidative stress, and in the regulation of redox-related calcium homeostasis. Mutations in this gene are associated with early onset muscle disorders, referred to as SEPN1-related myopathy. SEPN1-related myopathy consists of 4 autosomal recessive disorders, originally thought to be separate entities: rigid spine muscular dystrophy (RSMD1), the classical form of multiminicore disease, desmin related myopathy with Mallory-body like inclusions, and congenital fiber-type disproportion (CFTD). This protein is a selenoprotein, containing the rare amino acid selenocysteine (Sec). Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. A second stop-codon redefinition element (SRE) adjacent to the UGA codon has been identified in this gene (PMID:15791204). SRE is a phylogenetically conserved stem-loop structure that stimulates readthrough at the UGA codon, and augments the Sec insertion efficiency by SECIS. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2016]
Expression
Ubiquitous expression in prostate (RPKM 28.6), lung (RPKM 27.8) and 25 other tissues See more
Orthologs
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Genomic context

See SELENON in Genome Data Viewer
Location:
1p36.11
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (25800193..25818221)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (25637681..25655660)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (26126684..26144712)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25875990-25876603 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25889735-25890362 Neighboring gene low density lipoprotein receptor adaptor protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25893282-25894005 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25894006-25894730 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25894731-25895454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25900468-25901335 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25903029-25903950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25903951-25904872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25908041-25908889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25910781-25911344 Neighboring gene Sharpr-MPRA regulatory region 3419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 458 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25947842-25948342 Neighboring gene MPRA-validated peak129 silencer Neighboring gene mannosidase alpha class 1C member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 462 Neighboring gene MPRA-validated peak130 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 463 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:26019008-26019256 Neighboring gene Sharpr-MPRA regulatory region 1026 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:26030010-26030510 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:26030511-26031011 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26032137-26033112 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26033113-26034088 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26034089-26035064 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26035065-26036040 Neighboring gene MPRA-validated peak132 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26050687-26051187 Neighboring gene NANOG hESC enhancer GRCh37_chr1:26051273-26051916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26074639-26075196 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26075197-26075754 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:26076313-26076868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26078211-26078710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26083919-26084418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26098327-26099299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 465 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26106463-26107085 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26107086-26107708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26110213-26110835 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26125878-26126599 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26137118-26137992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26144488-26144988 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 467 Neighboring gene uncharacterized LOC646471 Neighboring gene mitochondrial fission regulator 1 like Neighboring gene hESC enhancers GRCh37_chr1:26185603-26186228 and GRCh37_chr1:26186229-26186854 Neighboring gene aurora kinase A and ninein interacting protein

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

Potential readthrough

Included gene: MTFR1L

Clone Names

  • FLJ24021

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in calcium ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in calcium ion homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cellular response to caffeine IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to oxidative stress IEA
Inferred from Electronic Annotation
more info
 
involved_in lung alveolus development IEA
Inferred from Electronic Annotation
more info
 
involved_in mitochondrion organization IEA
Inferred from Electronic Annotation
more info
 
involved_in multicellular organismal response to stress IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of response to oxidative stress IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of skeletal muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of ryanodine-sensitive calcium-release channel activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in respiratory system process IEA
Inferred from Electronic Annotation
more info
 
involved_in response to muscle activity involved in regulation of muscle adaptation IEA
Inferred from Electronic Annotation
more info
 
involved_in skeletal muscle fiber development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in skeletal muscle satellite cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
selenoprotein N
Names
selenoprotein N, 1

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.

Genomic

  1. NG_009930.1 RefSeqGene

    Range
    5018..23046
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_857

mRNA and Protein(s)

  1. NM_020451.3NP_065184.2  selenoprotein N isoform 2

    See identical proteins and their annotated locations for NP_065184.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an additional in-frame, Alu-derived coding exon in the 5' region compared to variant 1. The encoded isoform (2) is longer than isoform 1, containing two potential selenocysteine (Sec) residues. The first Sec found in the novel exon is not conserved, while the second Sec is highly conserved. Expression of isoform 2 was not detected in vivo or in transfection studies, leaving open the possibility that the UGA codon in the novel exon may be recognized as a stop codon, and not as a Sec codon (PMID:12700173).
    Source sequence(s)
    AA613025, AJ306399, BC021028, BQ217758
    Consensus CDS
    CCDS41282.1
    UniProtKB/Swiss-Prot
    A6NJG8, A8MQ64, Q6PI70, Q969F6, Q9NUI6, Q9NZV5
    UniProtKB/TrEMBL
    H9KV50
    Related
    ENSP00000355141.2, ENST00000361547.7
  2. NM_206926.2NP_996809.1  selenoprotein N isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes the canonical isoform (1).
    Source sequence(s)
    AA613025, AJ306399, BC021028, BQ217758
    Consensus CDS
    CCDS41283.1
    UniProtKB/TrEMBL
    H9KV50
    Related
    ENSP00000363434.1, ENST00000374315.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    25800193..25818221
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    25637681..25655660
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)