Human Gene LTBP3 (uc010rok.1)
  Description: Homo sapiens latent transforming growth factor beta binding protein 3 (LTBP3), transcript variant 1, mRNA.
RefSeq Summary (NM_001130144): The protein encoded by this gene forms a complex with transforming growth factor beta (TGF-beta) proteins and may be involved in their subcellular localization. Activation of this complex requires removal of the encoded binding protein. This protein also may play a structural role in the extracellular matrix. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010].
Transcript (Including UTRs)
   Position: hg19 chr11:65,306,882-65,326,253 Size: 19,372 Total Exon Count: 28 Strand: -
Coding Region
   Position: hg19 chr11:65,306,886-65,325,163 Size: 18,278 Coding Exon Count: 27 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviews
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:65,306,882-65,326,253)mRNA (may differ from genome)Protein (1134 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMalacardsMGIneXtProt
PubMedReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: LTBP3_HUMAN
DESCRIPTION: RecName: Full=Latent-transforming growth factor beta-binding protein 3; Short=LTBP-3; Flags: Precursor;
FUNCTION: May be involved in the assembly, secretion and targeting of TGFB1 to sites at which it is stored and/or activated. May play critical roles in controlling and directing the activity of TGFB1. May have a structural role in the extra cellular matrix (ECM).
SUBUNIT: Forms part of the large latent transforming growth factor beta precursor complex; removal is essential for activation of complex.
SUBCELLULAR LOCATION: Secreted (By similarity). Note=Secretion occurs after coexpression with TGFB1 and requires complexing with 'Cys-33' of the TGFB1 propeptide (By similarity).
TISSUE SPECIFICITY: Isoform 2 is expressed prominently in heart, skeletal muscle, prostate, testis, small intestine and ovary. Isoform 1 is strongly expressed in pancreas and liver.
PTM: Contains hydroxylated asparagine residues (By similarity).
PTM: Two intrachain disulfide bonds from the TB3 domain are rearranged upon TGFB1 binding, and form interchain bonds with TGFB1 propeptide, anchoring it to the extracellular matrix.
DISEASE: Defects in LTBP3 are the cause of tooth agenesis selective type 6 (STHAG6) [MIM:613097]. A form of selective tooth agenesis, a common anomaly characterized by the congenital absence of one or more teeth. Selective tooth agenesis without associated systemic disorders has sometimes been divided into 2 types: oligodontia, defined as agenesis of 6 or more permanent teeth, and hypodontia, defined as agenesis of less than 6 teeth. The number in both cases does not include absence of third molars (wisdom teeth). Some individuals affected by tooth agenesis selective type 6 have short stature.
SIMILARITY: Belongs to the LTBP family.
SIMILARITY: Contains 13 EGF-like domains.
SIMILARITY: Contains 4 TB (TGF-beta binding) domains.
SEQUENCE CAUTION: Sequence=BAB15767.1; Type=Erroneous initiation;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LTBP3
CDC HuGE Published Literature: LTBP3

-  MalaCards Disease Associations
  MalaCards Gene Search: LTBP3
Diseases sorted by gene-association score: dental anomalies and short stature* (1369), verloes bourguignon syndrome* (400), geleophysic dysplasia* (202), brachyolmia (16), amyotrophic lateral sclerosis 20 (11), amyotrophic lateral sclerosis type 10 (9), hypoplastic amelogenesis imperfecta (7), amyotrophic lateral sclerosis 7 (5), miles-carpenter syndrome (5), spinocerebellar ataxia 2 (5), separation anxiety disorder (5), amyotrophic lateral sclerosis 1 (1)
* = 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: 126.72 RPKM in Artery - Aorta
Total median expression: 1727.90 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 -86.20198-0.435 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
IPR000742 - EG-like_dom
IPR001881 - EGF-like_Ca-bd
IPR013032 - EGF-like_CS
IPR000152 - EGF-type_Asp/Asn_hydroxyl_site
IPR018097 - EGF_Ca-bd_CS
IPR017878 - TB_dom

Pfam Domains:
PF00683 - TB domain
PF07645 - Calcium-binding EGF domain
PF12661 - Human growth factor-like EGF
PF12662 - Complement Clr-like EGF-like

SCOP Domains:
57581 - TB module/8-cys domain
57196 - EGF/Laminin
57184 - Growth factor receptor domain

ModBase Predicted Comparative 3D Structure on Q9NS15
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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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0019838 growth factor binding
GO:0050431 transforming growth factor beta binding

Biological Process:
GO:0036363 transforming growth factor beta activation
GO:1902462 positive regulation of mesenchymal stem cell proliferation
GO:2000741 positive regulation of mesenchymal stem cell differentiation

Cellular Component:
GO:0005576 extracellular region
GO:0031012 extracellular matrix
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF211179 - JP 2014500723-A/18682: Polycomb-Associated Non-Coding RNAs.
AF318354 - Homo sapiens pp6425 mRNA, complete cds.
AF135960 - Homo sapiens latent transforming growth factor beta binding protein 3 mRNA, complete cds.
AK126126 - Homo sapiens cDNA FLJ44138 fis, clone THYMU2011736, highly similar to Homo sapiens latent transforming growth factor beta binding protein 3 (LTBP3).
AL117551 - Homo sapiens mRNA; cDNA DKFZp586M2123 (from clone DKFZp586M2123); partial cds.
BC008761 - Homo sapiens latent transforming growth factor beta binding protein 3, mRNA (cDNA clone IMAGE:3349420), partial cds.
AK097212 - Homo sapiens cDNA FLJ39893 fis, clone SPLEN2016743, highly similar to Latent transforming growth factor beta binding protein 3.
AK090750 - Homo sapiens cDNA FLJ33431 fis, clone BRACE2021143, highly similar to Homo sapiens latent transforming growth factor beta binding protein 3 mRNA.
AK124524 - Homo sapiens cDNA FLJ42533 fis, clone BRACE3003192, highly similar to Latent-transforming growth factor beta-binding protein 3 precursor.
AK024477 - Homo sapiens FLJ00070 mRNA for FLJ00070 protein.
BC136277 - Homo sapiens latent transforming growth factor beta binding protein 3, mRNA (cDNA clone MGC:167887 IMAGE:9020264), complete cds.
AK298858 - Homo sapiens cDNA FLJ55349 complete cds, highly similar to Latent-transforming growth factor beta-binding protein 3 precursor.
AB384415 - Synthetic construct DNA, clone: pF1KSDF0070, Homo sapiens LTBP3 gene for latent-transforming growth factor beta-binding protein 3 precursor, complete cds, without stop codon, in Flexi system.
AK299351 - Homo sapiens cDNA FLJ59398 complete cds, highly similar to Latent-transforming growth factor beta-binding protein 3 precursor.
LF344438 - JP 2014500723-A/151941: Polycomb-Associated Non-Coding RNAs.
AF135961 - Homo sapiens latent transforming growth factor beta binding protein 3 mRNA, partial cds, alternatively spliced.
LF344437 - JP 2014500723-A/151940: Polycomb-Associated Non-Coding RNAs.
LF344436 - JP 2014500723-A/151939: Polycomb-Associated Non-Coding RNAs.
LF344435 - JP 2014500723-A/151938: Polycomb-Associated Non-Coding RNAs.
AK127484 - Homo sapiens cDNA FLJ45576 fis, clone BRTHA3011229.
LF344434 - JP 2014500723-A/151937: Polycomb-Associated Non-Coding RNAs.
AF011407 - Homo sapiens latent TGF beta binding protein 3 (LTBP-3) mRNA, partial cds.
LF344431 - JP 2014500723-A/151934: Polycomb-Associated Non-Coding RNAs.
LF344430 - JP 2014500723-A/151933: Polycomb-Associated Non-Coding RNAs.
AK309230 - Homo sapiens cDNA, FLJ99271.
LF344429 - JP 2014500723-A/151932: Polycomb-Associated Non-Coding RNAs.
LF344428 - JP 2014500723-A/151931: Polycomb-Associated Non-Coding RNAs.
LF344427 - JP 2014500723-A/151930: Polycomb-Associated Non-Coding RNAs.
LF212762 - JP 2014500723-A/20265: Polycomb-Associated Non-Coding RNAs.
MA580015 - JP 2018138019-A/151941: Polycomb-Associated Non-Coding RNAs.
MA580014 - JP 2018138019-A/151940: Polycomb-Associated Non-Coding RNAs.
MA580013 - JP 2018138019-A/151939: Polycomb-Associated Non-Coding RNAs.
MA580012 - JP 2018138019-A/151938: Polycomb-Associated Non-Coding RNAs.
MA580011 - JP 2018138019-A/151937: Polycomb-Associated Non-Coding RNAs.
MA580008 - JP 2018138019-A/151934: Polycomb-Associated Non-Coding RNAs.
MA580007 - JP 2018138019-A/151933: Polycomb-Associated Non-Coding RNAs.
MA580006 - JP 2018138019-A/151932: Polycomb-Associated Non-Coding RNAs.
MA580005 - JP 2018138019-A/151931: Polycomb-Associated Non-Coding RNAs.
MA580004 - JP 2018138019-A/151930: Polycomb-Associated Non-Coding RNAs.
MA446756 - JP 2018138019-A/18682: Polycomb-Associated Non-Coding RNAs.
MA448339 - JP 2018138019-A/20265: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9NS15 (Reactome details) participates in the following event(s):

R-HSA-2395328 LTBP1, LTBP3 bind TGF-Beta
R-HSA-2328033 Fibrillin-1 binds latent TGF-beta
R-HSA-2129379 Molecules associated with elastic fibres
R-HSA-1566948 Elastic fibre formation
R-HSA-1474244 Extracellular matrix organization

-  Other Names for This Gene
  Alternate Gene Symbols: AK299351, LTBP3_HUMAN, O15107, Q96HB9, Q9H7K2, Q9NS15, Q9UFN4
UCSC ID: uc010rok.1
RefSeq Accession: NM_001130144
Protein: Q9NS15 (aka LTBP3_HUMAN or LTB3_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene LTBP3:
geleophys-dysp (Geleophysic Dysplasia)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK299351.1
exon count: 28CDS single in 3' UTR: no RNA size: 3608
ORF size: 3405CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 6878.00frame 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: no # 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.