Human Gene LMOD1 (uc021phl.1) Description and Page Index
  Description: Homo sapiens leiomodin 1 (smooth muscle) (LMOD1), mRNA.
RefSeq Summary (NM_012134): The leiomodin 1 protein has a putative membrane-spanning region and 2 types of tandemly repeated blocks. The transcript is expressed in all tissues tested, with the highest levels in thyroid, eye muscle, skeletal muscle, and ovary. Increased expression of leiomodin 1 may be linked to Graves' disease and thyroid-associated ophthalmopathy. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC080187.1, X54162.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2144333, SAMEA2146411 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000367288.5/ ENSP00000356257.4 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr1:201,865,584-201,915,716 Size: 50,133 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr1:201,867,406-201,915,468 Size: 48,063 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:201,865,584-201,915,716)mRNA (may differ from genome)Protein (600 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: LMOD1_HUMAN
DESCRIPTION: RecName: Full=Leiomodin-1; AltName: Full=64 kDa autoantigen 1D; AltName: Full=64 kDa autoantigen 1D3; AltName: Full=64 kDa autoantigen D1; AltName: Full=Leiomodin, muscle form; AltName: Full=Smooth muscle leiomodin; Short=SM-Lmod; AltName: Full=Thyroid-associated ophthalmopathy autoantigen;
SUBCELLULAR LOCATION: Cytoplasm. Cytoplasm, cytoskeleton.
TISSUE SPECIFICITY: Smooth muscle (heart, skeletal muscle, colon and small intestine), a subset of striated muscle fibers, and at low level in thyroid.
SIMILARITY: Belongs to the tropomodulin family.
SIMILARITY: Contains 1 WH2 domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LMOD1
CDC HuGE Published Literature: LMOD1
Positive Disease Associations: Parkinson Disease
Related Studies:
  1. Parkinson Disease
    Hon-Chung Fung et al. Lancet neurology 2006, Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data., Lancet neurology. [PubMed 17052657]
    We generated publicly available genotype data for Parkinsons disease patients and controls so that these data can be mined and augmented by other researchers to identify common genetic variability that results in minor and moderate risk for disease.

-  MalaCards Disease Associations
  MalaCards Gene Search: LMOD1
Diseases sorted by gene-association score: moved to 155310* (202), graves' disease (15), leukodystrophy, hypomyelinating, 13 (12), leukodystrophy, hypomyelinating, 8, with or without oligodontia and/or hypogonadotropic hypogonadism (12), cardiomyopathy, hypertrophic 6 (12), visceral myopathy (7), steroid-induced glaucoma (7), coronary restenosis (7), ethylmalonic encephalopathy (6), hyperthyroidism (6), thyroid cancer, nonmedullary, 2 (2)
* = Manually curated disease association

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

+  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: 601.79 RPKM in Artery - Tibial
Total median expression: 4744.28 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 -89.81248-0.362 Picture PostScript Text
3' UTR -744.101822-0.408 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
IPR004934 - Tropomodulin
IPR003124 - WH2_dom

Pfam Domains:
PF02205 - WH2 motif
PF03250 - Tropomodulin
PF13516 - Leucine Rich repeat

SCOP Domains:
52047 - RNI-like

ModBase Predicted Comparative 3D Structure on P29536
FrontTopSide
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0005523 tropomyosin binding

Biological Process:
GO:0006936 muscle contraction
GO:0030239 myofibril assembly
GO:0030838 positive regulation of actin filament polymerization
GO:0045010 actin nucleation
GO:0051694 pointed-end actin filament capping

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005865 striated muscle thin filament
GO:0005884 actin filament
GO:0016020 membrane
GO:0030016 myofibril
GO:0030017 sarcomere


-  Descriptions from all associated GenBank mRNAs
  X54162 - Human mRNA for a 64 Kd autoantigen expressed in thyroid and extra-ocular muscle.
JD267311 - Sequence 248335 from Patent EP1572962.
BC080187 - Homo sapiens leiomodin 1 (smooth muscle), mRNA (cDNA clone MGC:87977 IMAGE:6177902), complete cds.
AK126474 - Homo sapiens cDNA FLJ44510 fis, clone UTERU3001652, highly similar to Leiomodin-1.
JD512444 - Sequence 493468 from Patent EP1572962.
JD371155 - Sequence 352179 from Patent EP1572962.
JD387055 - Sequence 368079 from Patent EP1572962.
JD084315 - Sequence 65339 from Patent EP1572962.
JD113437 - Sequence 94461 from Patent EP1572962.
JD504747 - Sequence 485771 from Patent EP1572962.
JD426369 - Sequence 407393 from Patent EP1572962.
JD079915 - Sequence 60939 from Patent EP1572962.
JD420061 - Sequence 401085 from Patent EP1572962.
JD190736 - Sequence 171760 from Patent EP1572962.
JD078085 - Sequence 59109 from Patent EP1572962.
JD471639 - Sequence 452663 from Patent EP1572962.
JD247858 - Sequence 228882 from Patent EP1572962.
JD546658 - Sequence 527682 from Patent EP1572962.
JD038997 - Sequence 20021 from Patent EP1572962.
JD167824 - Sequence 148848 from Patent EP1572962.
JD351934 - Sequence 332958 from Patent EP1572962.
JD114537 - Sequence 95561 from Patent EP1572962.
JD121933 - Sequence 102957 from Patent EP1572962.
JD192377 - Sequence 173401 from Patent EP1572962.
JD132017 - Sequence 113041 from Patent EP1572962.
JD463387 - Sequence 444411 from Patent EP1572962.
JD146293 - Sequence 127317 from Patent EP1572962.
JD350037 - Sequence 331061 from Patent EP1572962.
JD346914 - Sequence 327938 from Patent EP1572962.
JD076399 - Sequence 57423 from Patent EP1572962.
JD170411 - Sequence 151435 from Patent EP1572962.
JD491856 - Sequence 472880 from Patent EP1572962.
JD453814 - Sequence 434838 from Patent EP1572962.
JD512987 - Sequence 494011 from Patent EP1572962.
JD090822 - Sequence 71846 from Patent EP1572962.
JD188151 - Sequence 169175 from Patent EP1572962.
JD373769 - Sequence 354793 from Patent EP1572962.
JD346880 - Sequence 327904 from Patent EP1572962.
JD474446 - Sequence 455470 from Patent EP1572962.
JD348757 - Sequence 329781 from Patent EP1572962.
JD477097 - Sequence 458121 from Patent EP1572962.
JD107280 - Sequence 88304 from Patent EP1572962.
JD518644 - Sequence 499668 from Patent EP1572962.
JD304099 - Sequence 285123 from Patent EP1572962.
BC001755 - Homo sapiens leiomodin 1 (smooth muscle), mRNA (cDNA clone IMAGE:3355265), complete cds.
JD416781 - Sequence 397805 from Patent EP1572962.
JD520901 - Sequence 501925 from Patent EP1572962.
JD086324 - Sequence 67348 from Patent EP1572962.
JD320731 - Sequence 301755 from Patent EP1572962.
JD373168 - Sequence 354192 from Patent EP1572962.
JD478741 - Sequence 459765 from Patent EP1572962.
JD382185 - Sequence 363209 from Patent EP1572962.
JD277367 - Sequence 258391 from Patent EP1572962.
JD119142 - Sequence 100166 from Patent EP1572962.
JD144447 - Sequence 125471 from Patent EP1572962.
JD100820 - Sequence 81844 from Patent EP1572962.
JD184829 - Sequence 165853 from Patent EP1572962.
JD455295 - Sequence 436319 from Patent EP1572962.
JD381605 - Sequence 362629 from Patent EP1572962.
JD123475 - Sequence 104499 from Patent EP1572962.
JD365585 - Sequence 346609 from Patent EP1572962.
JD115796 - Sequence 96820 from Patent EP1572962.
JD372404 - Sequence 353428 from Patent EP1572962.
JD172632 - Sequence 153656 from Patent EP1572962.
AK304852 - Homo sapiens cDNA FLJ53443 complete cds, highly similar to Leiomodin-1.
AK304700 - Homo sapiens cDNA FLJ54257 complete cds, highly similar to Leiomodin-1.
JD044605 - Sequence 25629 from Patent EP1572962.
JD400233 - Sequence 381257 from Patent EP1572962.
JD162616 - Sequence 143640 from Patent EP1572962.
AK295824 - Homo sapiens cDNA FLJ55689 complete cds, highly similar to Leiomodin-1.
JD088001 - Sequence 69025 from Patent EP1572962.
JD473719 - Sequence 454743 from Patent EP1572962.
JD439216 - Sequence 420240 from Patent EP1572962.
KJ906100 - Synthetic construct Homo sapiens clone ccsbBroadEn_15770 LMOD1 gene, encodes complete protein.
AK311740 - Homo sapiens cDNA, FLJ18782.
CU687334 - Synthetic construct Homo sapiens gateway clone IMAGE:100022958 5' read LMOD1 mRNA.
JD518874 - Sequence 499898 from Patent EP1572962.
JD317462 - Sequence 298486 from Patent EP1572962.
JD098270 - Sequence 79294 from Patent EP1572962.

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

Protein P29536 (Reactome details) participates in the following event(s):

R-HSA-445705 Release Of ADP From Myosin
R-HSA-445699 ATP Hydrolysis By Myosin
R-HSA-445700 Myosin Binds ATP
R-HSA-445704 Calcium Binds Caldesmon
R-HSA-445355 Smooth Muscle Contraction
R-HSA-397014 Muscle contraction

-  Other Names for This Gene
  Alternate Gene Symbols: B1APV6, C4AMB1, LMOD1_HUMAN, NM_012134, NP_036266, P29536, Q68EN2
UCSC ID: uc021phl.1
RefSeq Accession: NM_012134
Protein: P29536 (aka LMOD1_HUMAN)
CCDS: CCDS53457.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_012134.2
exon count: 3CDS single in 3' UTR: no RNA size: 3967
ORF size: 1896CDS single in intron: no Alignment % ID: 99.97
txCdsPredict score: 3992.00frame shift in genome: no % Coverage: 99.97
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.