Human Gene LEMD3 (ENST00000308330.3_4) from GENCODE V47lift37
  Description: LEM domain containing 3, transcript variant 1 (from RefSeq NM_014319.5)
Gencode Transcript: ENST00000308330.3_4
Gencode Gene: ENSG00000174106.3_8
Transcript (Including UTRs)
   Position: hg19 chr12:65,563,363-65,642,135 Size: 78,773 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr12:65,563,377-65,640,105 Size: 76,729 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:65,563,363-65,642,135)mRNA (may differ from genome)Protein (911 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MAN1_HUMAN
DESCRIPTION: RecName: Full=Inner nuclear membrane protein Man1; AltName: Full=LEM domain-containing protein 3;
FUNCTION: Can function as a specific repressor of TGF-beta, activin, and BMP signaling through its interaction with the R-SMAD proteins. Antagonizes TGF-beta-induced cell proliferation arrest.
SUBUNIT: Interacts with SMAD1, SMAD2, SMAD3 and SMAD5. Binds to both phosphorylated and unphosphorylated R-SMADS.
SUBCELLULAR LOCATION: Nucleus inner membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Heart, brain, placenta, lung, liver and skeletal muscle.
DISEASE: Defects in LEMD3 are the cause of Buschke-Ollendorff syndrome (BOS) [MIM:166700]; also known as dermatoosteopoikilosis or disseminated dermatofibrosis with osteopoikilosis or dermatofibrosis lenticularis disseminata with osteopoikilosis or osteopathia condensans disseminata. BOS refers to the association of osteopoikilosis with disseminated connective-tissue nevi. Osteopoikilosis is a skeletal dysplasia characterized by a symmetric but unequal distribution of multiple hyperostotic areas in different parts of the skeleton. Both elastic-type nevi (juvenile elastoma) and collagen-type nevi (dermatofibrosis lenticularis disseminata) have been described in BOS. Skin or bony lesions can be absent in some family members, whereas other relatives may have both.
DISEASE: Defects in LEMD3 are a cause of melorheostosis (MEL) [MIM:155950]. Melorheostosis is a rare mesenchymal dysplasia and one of the sclerosing bone disorders. It is caused by a developmental error, with a sclerotomal distribution, frequently involving one limb. It may be asymptomatic, but pain, stiffness with limitation of motion, leg-length discrepancy and limb deformity may occur.
SIMILARITY: Contains 1 LEM domain.

-  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.
Click here to open Exonprimer with this transcript

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: LEMD3
Diseases sorted by gene-association score: buschke-ollendorff syndrome* (1402), melorheostosis with osteopoikilosis* (850), osteopoikilosis* (460), melorheostosis (57), elastoma (18), 12q14 microdeletion syndrome* (18), glomangiomatosis (9), emery-dreifuss muscular dystrophy (9), cardiovascular organ benign neoplasm (8), benign perivascular tumor (8), hyperostosis, endosteal (6), bone remodeling disease (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.10 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 325.30 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
3' UTR -488.902030-0.241 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
IPR018996 - Inner-Nucl-membr_MAN1
IPR003887 - LEM
IPR011015 - LEM-like_dom
IPR012677 - Nucleotide-bd_a/b_plait

Pfam Domains:
PF03020 - LEM domain
PF09402 - Man1-Src1p-C-terminal domain

SCOP Domains:
63451 - LEM domain
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2CH0 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9Y2U8
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0031490 chromatin DNA binding

Biological Process:
GO:0001525 angiogenesis
GO:0006997 nucleus organization
GO:0006998 nuclear envelope organization
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway
GO:0030514 negative regulation of BMP signaling pathway
GO:0032926 negative regulation of activin receptor signaling pathway
GO:0070197 meiotic attachment of telomere to nuclear envelope
GO:1902531 regulation of intracellular signal transduction

Cellular Component:
GO:0005634 nucleus
GO:0005637 nuclear inner membrane
GO:0005639 integral component of nuclear inner membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031965 nuclear membrane


-  Descriptions from all associated GenBank mRNAs
  AK312473 - Homo sapiens cDNA, FLJ92831.
LF385459 - JP 2014500723-A/192962: Polycomb-Associated Non-Coding RNAs.
AK304317 - Homo sapiens cDNA FLJ56676 complete cds, highly similar to Inner nuclear membrane protein Man1.
LF208908 - JP 2014500723-A/16411: Polycomb-Associated Non-Coding RNAs.
AF112299 - Homo sapiens integral inner nuclear membrane protein MAN1 mRNA, complete cds.
BC167864 - Synthetic construct Homo sapiens clone IMAGE:100068254, MGC:195871 LEM domain containing 3 (LEMD3) mRNA, encodes complete protein.
LF323992 - JP 2014500723-A/131495: Polycomb-Associated Non-Coding RNAs.
LF323991 - JP 2014500723-A/131494: Polycomb-Associated Non-Coding RNAs.
LF323990 - JP 2014500723-A/131493: Polycomb-Associated Non-Coding RNAs.
LF323989 - JP 2014500723-A/131492: Polycomb-Associated Non-Coding RNAs.
AK024954 - Homo sapiens cDNA: FLJ21301 fis, clone COL02065, highly similar to AF112299 Homo sapiens integral inner nuclear membrane protein MAN1 mRNA.
LF323988 - JP 2014500723-A/131491: Polycomb-Associated Non-Coding RNAs.
KY966263 - Homo sapiens cell line 95T1000 LEMD3/MKX fusion mRNA, partial sequence.
LF323987 - JP 2014500723-A/131490: Polycomb-Associated Non-Coding RNAs.
LF323974 - JP 2014500723-A/131477: Polycomb-Associated Non-Coding RNAs.
LF323970 - JP 2014500723-A/131473: Polycomb-Associated Non-Coding RNAs.
AK295406 - Homo sapiens cDNA FLJ56612 complete cds, highly similar to Inner nuclear membrane protein Man1.
LF323967 - JP 2014500723-A/131470: Polycomb-Associated Non-Coding RNAs.
LF323966 - JP 2014500723-A/131469: Polycomb-Associated Non-Coding RNAs.
AL137533 - Homo sapiens mRNA; cDNA DKFZp434G1919 (from clone DKFZp434G1919); partial cds.
LF323965 - JP 2014500723-A/131468: Polycomb-Associated Non-Coding RNAs.
LF323964 - JP 2014500723-A/131467: Polycomb-Associated Non-Coding RNAs.
JD093470 - Sequence 74494 from Patent EP1572962.
JD453969 - Sequence 434993 from Patent EP1572962.
JD357396 - Sequence 338420 from Patent EP1572962.
JD565055 - Sequence 546079 from Patent EP1572962.
JD465747 - Sequence 446771 from Patent EP1572962.
JD424871 - Sequence 405895 from Patent EP1572962.
JD509926 - Sequence 490950 from Patent EP1572962.
JD022214 - Sequence 3238 from Patent EP1572962.
JD283605 - Sequence 264629 from Patent EP1572962.
JD033004 - Sequence 14028 from Patent EP1572962.
JD019181 - Sequence 205 from Patent EP1572962.
JD034032 - Sequence 15056 from Patent EP1572962.
JD302739 - Sequence 283763 from Patent EP1572962.
JD263994 - Sequence 245018 from Patent EP1572962.
JD303649 - Sequence 284673 from Patent EP1572962.
LF323963 - JP 2014500723-A/131466: Polycomb-Associated Non-Coding RNAs.
JD509430 - Sequence 490454 from Patent EP1572962.
JD069154 - Sequence 50178 from Patent EP1572962.
JD416720 - Sequence 397744 from Patent EP1572962.
MA621036 - JP 2018138019-A/192962: Polycomb-Associated Non-Coding RNAs.
MA559569 - JP 2018138019-A/131495: Polycomb-Associated Non-Coding RNAs.
MA559568 - JP 2018138019-A/131494: Polycomb-Associated Non-Coding RNAs.
MA559567 - JP 2018138019-A/131493: Polycomb-Associated Non-Coding RNAs.
MA559566 - JP 2018138019-A/131492: Polycomb-Associated Non-Coding RNAs.
MA559565 - JP 2018138019-A/131491: Polycomb-Associated Non-Coding RNAs.
MA559564 - JP 2018138019-A/131490: Polycomb-Associated Non-Coding RNAs.
MA559551 - JP 2018138019-A/131477: Polycomb-Associated Non-Coding RNAs.
MA559547 - JP 2018138019-A/131473: Polycomb-Associated Non-Coding RNAs.
MA559544 - JP 2018138019-A/131470: Polycomb-Associated Non-Coding RNAs.
MA559543 - JP 2018138019-A/131469: Polycomb-Associated Non-Coding RNAs.
MA559542 - JP 2018138019-A/131468: Polycomb-Associated Non-Coding RNAs.
MA559541 - JP 2018138019-A/131467: Polycomb-Associated Non-Coding RNAs.
MA559540 - JP 2018138019-A/131466: Polycomb-Associated Non-Coding RNAs.
MA444485 - JP 2018138019-A/16411: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y2U8 (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: ENST00000308330.1, ENST00000308330.2, MAN1, MAN1_HUMAN, NM_014319, Q9NT47, Q9NYA5, Q9Y2U8, uc317oha.1, uc317oha.2
UCSC ID: ENST00000308330.3_4
RefSeq Accession: NM_014319.5
Protein: Q9Y2U8 (aka MAN1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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