Human Gene EMD (ENST00000369842.9) from GENCODE V44
  Description: Homo sapiens emerin (EMD), mRNA. (from RefSeq NM_000117)
RefSeq Summary (NM_000117): Emerin is a serine-rich nuclear membrane protein and a member of the nuclear lamina-associated protein family. It mediates membrane anchorage to the cytoskeleton. Dreifuss-Emery muscular dystrophy is an X-linked inherited degenerative myopathy resulting from mutation in the emerin gene. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000369842.9
Gencode Gene: ENSG00000102119.12
Transcript (Including UTRs)
   Position: hg38 chrX:154,379,295-154,381,523 Size: 2,229 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg38 chrX:154,379,485-154,381,197 Size: 1,713 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:154,379,295-154,381,523)mRNA (may differ from genome)Protein (254 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: EMD_HUMAN
DESCRIPTION: RecName: Full=Emerin;
FUNCTION: Stabilizes and promotes the formation of a nuclear actin cortical network. Stimulates actin polymerization in vitro by binding and stabilizing the pointed end of growing filaments. Inhibits beta-catenin activity by preventing its accumulation in the nucleus. Acts by influencing the nuclear accumulation of beta- catenin through a CRM1-dependent export pathway. Links centrosomes to the nuclear envelope via a microtubule association. EMD and BAF are cooperative cofactors of HIV-1 infection. Association of EMD with the viral DNA requires the presence of BAF and viral integrase. The association of viral DNA with chromatin requires the presence of BAF and EMD. Required for proper localization of non-farnesylated prelamin-A/C.
SUBUNIT: Interacts with lamins A and C, BANF1, GMCL, BCLAF1 and YTHDC1/YT521. Interacts with TMEM43; the interaction retains emerin in the nuclear inner membrane. Interacts with SUN1 and SUN2 (By similarity). Interacts with ACTB, SPTAN1, F-actin, CTNNB1 and beta-tubulin.
INTERACTION: Q9NYF8:BCLAF1; NbExp=3; IntAct=EBI-489887, EBI-437804; Q99962:SH3GL2; NbExp=2; IntAct=EBI-489887, EBI-77938;
SUBCELLULAR LOCATION: Nucleus inner membrane; Single-pass membrane protein; Nucleoplasmic side. Nucleus outer membrane. Note=Colocalized with BANF1 at the central region of the assembling nuclear rim, near spindle-attachment sites. The accumulation of different intermediates of prelamin-A/C (non- farnesylated or carboxymethylated farnesylated prelamin-A/C) in fibroblasts modify its localization in the nucleus.
TISSUE SPECIFICITY: Skeletal muscle, heart, colon, testis, ovary and pancreas.
PTM: Found in four different phosphorylated forms, three of which appear to be associated with the cell cycle.
DISEASE: Defects in EMD are the cause of Emery-Dreifuss muscular dystrophy type 1 (EDMD1) [MIM:310300]. A degenerative myopathy characterized by weakness and atrophy of muscle without involvement of the nervous system, early contractures of the elbows Achilles tendons and spine, and cardiomyopathy associated with cardiac conduction defects.
SIMILARITY: Contains 1 LEM domain.
WEB RESOURCE: Name=EMD db; Note="EMD mutation database"; URL="http://www.dmd.nl/nmdb/index.php?select_db=EMD";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/EMD";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: EMD
Diseases sorted by gene-association score: emery-dreifuss muscular dystrophy 1, x-linked* (1231), emery-dreifuss muscular dystrophy, x-linked* (750), emery-dreifuss muscular dystrophy* (125), emd-related emery-dreifuss muscular dystrophy, x-linked* (100), familial partial lipodystrophy (26), muscular dystrophy (25), emerinopathy (18), proximal myopathy and ophthalmoplegia (14), cardiomyopathy, dilated, 1a (12), autosomal dominant limb-girdle muscular dystrophy (10), emery-dreifuss muscular dystrophy 2, ad (10), cardiomyopathy, dilated, 1h (9), muscular dystrophy, limb-girdle, type 1b (8), dilated cardiomyopathy (8), congenital muscular dystrophy due to lmna mutation (8), myopathy (8), congenital fiber-type disproportion (6), cardiomyopathy (6), myopathy, x-linked, with excessive autophagy (6), secretory diarrhea (6), pelger-huet anomaly (6), atrial standstill, digenic (5), muscle tissue disease (4), myopathy, tubular aggregate, 1 (4), inclusion body myositis (3), neuromuscular disease (3), arrhythmogenic right ventricular cardiomyopathy (3)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 76.33 RPKM in Ovary
Total median expression: 2049.91 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -87.00190-0.458 Picture PostScript Text
3' UTR -134.30326-0.412 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003887 - LEM
IPR011015 - LEM-like_dom

Pfam Domains:
PF03020 - LEM domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1JEI - NMR 2ODC - NMR MuPIT 2ODG - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P50402
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0005515 protein binding
GO:0045296 cadherin binding
GO:0048487 beta-tubulin binding

Biological Process:
GO:0006936 muscle contraction
GO:0007084 mitotic nuclear envelope reassembly
GO:0007517 muscle organ development
GO:0035914 skeletal muscle cell differentiation
GO:0046827 positive regulation of protein export from nucleus
GO:0048147 negative regulation of fibroblast proliferation
GO:0060828 regulation of canonical Wnt signaling pathway
GO:0071363 cellular response to growth factor stimulus
GO:0090090 negative regulation of canonical Wnt signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005637 nuclear inner membrane
GO:0005640 nuclear outer membrane
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005874 microtubule
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031965 nuclear membrane
GO:0031616 spindle pole centrosome
GO:0032541 cortical endoplasmic reticulum


-  Descriptions from all associated GenBank mRNAs
  BC000738 - Homo sapiens emerin, mRNA (cDNA clone MGC:2126 IMAGE:3505626), complete cds.
X82434 - H.sapiens mRNA for emerin.
JD458436 - Sequence 439460 from Patent EP1572962.
AB463603 - Synthetic construct DNA, clone: pF1KB8315, Homo sapiens EMD gene for emerin, without stop codon, in Flexi system.
CU674378 - Synthetic construct Homo sapiens gateway clone IMAGE:100020640 5' read EMD mRNA.
KJ891107 - Synthetic construct Homo sapiens clone ccsbBroadEn_00501 EMD gene, encodes complete protein.
KR709801 - Synthetic construct Homo sapiens clone CCSBHm_00006159 EMD (EMD) mRNA, encodes complete protein.
KR709802 - Synthetic construct Homo sapiens clone CCSBHm_00006161 EMD (EMD) mRNA, encodes complete protein.
KR709803 - Synthetic construct Homo sapiens clone CCSBHm_00006171 EMD (EMD) mRNA, encodes complete protein.
KR709804 - Synthetic construct Homo sapiens clone CCSBHm_00006172 EMD (EMD) mRNA, encodes complete protein.
AM393723 - Synthetic construct Homo sapiens clone IMAGE:100002043 for hypothetical protein (EMD gene).
BT007401 - Homo sapiens emerin (Emery-Dreifuss muscular dystrophy) mRNA, complete cds.
CR536536 - Homo sapiens full open reading frame cDNA clone RZPDo834B0522D for gene EMD, emerin (Emery-Dreifuss muscular dystrophy); complete cds, incl. stopcodon.
JD164466 - Sequence 145490 from Patent EP1572962.
JD337342 - Sequence 318366 from Patent EP1572962.
JD242361 - Sequence 223385 from Patent EP1572962.
JD345864 - Sequence 326888 from Patent EP1572962.
JD243605 - Sequence 224629 from Patent EP1572962.
JD271642 - Sequence 252666 from Patent EP1572962.
JD370345 - Sequence 351369 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa05410 - Hypertrophic cardiomyopathy (HCM)
hsa05412 - Arrhythmogenic right ventricular cardiomyopathy (ARVC)
hsa05414 - Dilated cardiomyopathy

Reactome (by CSHL, EBI, and GO)

Protein P50402 (Reactome details) participates in the following event(s):

R-HSA-2995376 BANF1 binds chromatin, EMD/TMPO/LEMD3/LEMD2 and lamins
R-HSA-2993898 VRK1/VRK2 phosphorylate BANF1
R-HSA-2995383 Initiation of Nuclear Envelope Reformation
R-HSA-4419969 Depolymerisation of the Nuclear Lamina
R-HSA-2993913 Clearance of Nuclear Envelope Membranes from Chromatin
R-HSA-2995410 Nuclear Envelope Reassembly
R-HSA-2980766 Nuclear Envelope Breakdown
R-HSA-68882 Mitotic Anaphase
R-HSA-68875 Mitotic Prophase
R-HSA-2555396 Mitotic Metaphase and Anaphase
R-HSA-68886 M Phase
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: EDMD, EMD_HUMAN, ENST00000369842.1, ENST00000369842.2, ENST00000369842.3, ENST00000369842.4, ENST00000369842.5, ENST00000369842.6, ENST00000369842.7, ENST00000369842.8, NM_000117, P50402, Q6FI02, STA, uc004fkl.1, uc004fkl.2, uc004fkl.3, uc004fkl.4, uc004fkl.5
UCSC ID: ENST00000369842.9
RefSeq Accession: NM_000117
Protein: P50402 (aka EMD_HUMAN)
CCDS: CCDS14745.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene EMD:
edmd (Emery-Dreifuss Muscular Dystrophy)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.