Human Gene FMOD (ENST00000354955.5_7) from GENCODE V47lift37
  Description: fibromodulin, transcript variant 1 (from RefSeq NM_002023.5)
Gencode Transcript: ENST00000354955.5_7
Gencode Gene: ENSG00000122176.12_10
Transcript (Including UTRs)
   Position: hg19 chr1:203,309,756-203,320,250 Size: 10,495 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr1:203,311,471-203,317,398 Size: 5,928 Coding Exon Count: 2 

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 (chr1:203,309,756-203,320,250)mRNA (may differ from genome)Protein (376 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: FMOD_HUMAN
DESCRIPTION: RecName: Full=Fibromodulin; Short=FM; AltName: Full=Collagen-binding 59 kDa protein; AltName: Full=Keratan sulfate proteoglycan fibromodulin; Short=KSPG fibromodulin; Flags: Precursor;
FUNCTION: Affects the rate of fibrils formation. May have a primary role in collagen fibrillogenesis (By similarity).
SUBUNIT: Binds to type I and type II collagen (By similarity).
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix.
PTM: Binds keratan sulfate chains.
SIMILARITY: Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class II subfamily.
SIMILARITY: Contains 11 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 LRRNT 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: FMOD
Diseases sorted by gene-association score: myopia (6), chronic lymphocytic leukemia (2), pilocytic astrocytoma (2), corneal dystrophy, congenital stromal (2), achondrogenesis, type ii or hypochondrogenesis (2), kniest dysplasia (2), hypochondrogenesis (1)

-  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: 267.46 RPKM in Artery - Aorta
Total median expression: 1922.44 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 -20.7097-0.213 Picture PostScript Text
3' UTR -608.901715-0.355 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
IPR001611 - Leu-rich_rpt
IPR003591 - Leu-rich_rpt_typical-subtyp
IPR000372 - LRR-contain_N

Pfam Domains:
PF00560 - Leucine Rich Repeat
PF01462 - Leucine rich repeat N-terminal domain
PF13306 - BspA type Leucine rich repeat region (6 copies)
PF13855 - Leucine rich repeat

SCOP Domains:
141571 - Pentapeptide repeat-like
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1

ModBase Predicted Comparative 3D Structure on Q06828
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0007181 transforming growth factor beta receptor complex assembly
GO:0018146 keratan sulfate biosynthetic process
GO:0030199 collagen fibril organization
GO:0042340 keratan sulfate catabolic process
GO:0007409 axonogenesis

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005796 Golgi lumen
GO:0031012 extracellular matrix
GO:0043202 lysosomal lumen


-  Descriptions from all associated GenBank mRNAs
  X75546 - H.sapiens mRNA for fibromodulin.
AK092899 - Homo sapiens cDNA FLJ35580 fis, clone SPLEN2006389, highly similar to FIBROMODULIN PRECURSOR.
AX747797 - Sequence 1322 from Patent EP1308459.
BC035281 - Homo sapiens fibromodulin, mRNA (cDNA clone MGC:34457 IMAGE:5181410), complete cds.
GQ891412 - Homo sapiens clone HEL-S-133 epididymis secretory sperm binding protein mRNA, complete cds.
AK098322 - Homo sapiens cDNA FLJ41003 fis, clone UTERU2016981.
U05291 - Human fibromodulin mRNA, partial cds.
AK172740 - Homo sapiens cDNA PSEC0234 fis, clone: HEMBA1007044, highly similar to FIBROMODULIN PRECURSOR.
JD198677 - Sequence 179701 from Patent EP1572962.
JD191138 - Sequence 172162 from Patent EP1572962.
JD296746 - Sequence 277770 from Patent EP1572962.
JD464061 - Sequence 445085 from Patent EP1572962.
JD560028 - Sequence 541052 from Patent EP1572962.
JD419328 - Sequence 400352 from Patent EP1572962.
JD456508 - Sequence 437532 from Patent EP1572962.
JD353695 - Sequence 334719 from Patent EP1572962.
JD122929 - Sequence 103953 from Patent EP1572962.
JD231304 - Sequence 212328 from Patent EP1572962.
JD231303 - Sequence 212327 from Patent EP1572962.
JD388591 - Sequence 369615 from Patent EP1572962.
JD219633 - Sequence 200657 from Patent EP1572962.
JD155292 - Sequence 136316 from Patent EP1572962.
JD024547 - Sequence 5571 from Patent EP1572962.
JD101759 - Sequence 82783 from Patent EP1572962.
AK291632 - Homo sapiens cDNA FLJ75875 complete cds, highly similar to Homo sapiens fibromodulin (FMOD), mRNA.
JD317383 - Sequence 298407 from Patent EP1572962.
JD390986 - Sequence 372010 from Patent EP1572962.
JD188106 - Sequence 169130 from Patent EP1572962.
JD137221 - Sequence 118245 from Patent EP1572962.
JD230717 - Sequence 211741 from Patent EP1572962.
JD148835 - Sequence 129859 from Patent EP1572962.
JD287307 - Sequence 268331 from Patent EP1572962.
JD240113 - Sequence 221137 from Patent EP1572962.
JD322346 - Sequence 303370 from Patent EP1572962.
JD185809 - Sequence 166833 from Patent EP1572962.
JD086158 - Sequence 67182 from Patent EP1572962.
JD486476 - Sequence 467500 from Patent EP1572962.
JD102701 - Sequence 83725 from Patent EP1572962.
AK303866 - Homo sapiens cDNA FLJ53615 complete cds, highly similar to Fibromodulin precursor.
JD074791 - Sequence 55815 from Patent EP1572962.
JD144877 - Sequence 125901 from Patent EP1572962.
JD195501 - Sequence 176525 from Patent EP1572962.
KJ891190 - Synthetic construct Homo sapiens clone ccsbBroadEn_00584 FMOD gene, encodes complete protein.
DQ892112 - Synthetic construct clone IMAGE:100004742; FLH183135.01X; RZPDo839G04140D fibromodulin (FMOD) gene, encodes complete protein.
DQ895306 - Synthetic construct Homo sapiens clone IMAGE:100009766; FLH183131.01L; RZPDo839G04139D fibromodulin (FMOD) gene, encodes complete protein.
AB590335 - Synthetic construct DNA, clone: pFN21AE1465, Homo sapiens FMOD gene for fibromodulin, without stop codon, in Flexi system.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_slrpPathway - Small Leucine-rich Proteoglycan (SLRP) molecules

Reactome (by CSHL, EBI, and GO)

Protein Q06828 (Reactome details) participates in the following event(s):

R-HSA-2025724 B3GNT1,2,3,4,7 add GlcNAc to form Keratan-PG
R-HSA-2025723 B4GALTs transfer Gal to the N-glycan precursor
R-HSA-2046222 CHST2,5,6 transfer SO4(2-) to GlcNAc residues on keratan-PG to form KSPG
R-HSA-2046285 The keratan chain can be capped by N-acetylneuraminic acid
R-HSA-2046265 B4GALTs transfer Gal to the keratan chain
R-HSA-2327886 SLRPs bind TGF Beta
R-NUL-2466133 SLRPs bind TGF beta
R-HSA-2046175 Further sulfation on galactose residues produces KSPG
R-HSA-2046298 B4GALTs transfer Gal to a branch of keratan
R-HSA-2022854 Keratan sulfate biosynthesis
R-HSA-3656225 Defective CHST6 causes MCDC1
R-HSA-3656244 Defective B4GALT1 causes B4GALT1-CDG (CDG-2d)
R-HSA-2022857 Keratan sulfate degradation
R-HSA-3000178 ECM proteoglycans
R-HSA-3656243 Defective ST3GAL3 causes MCT12 and EIEE15
R-HSA-1638074 Keratan sulfate/keratin metabolism
R-HSA-3560782 Diseases associated with glycosaminoglycan metabolism
R-HSA-1474244 Extracellular matrix organization
R-HSA-1630316 Glycosaminoglycan metabolism
R-HSA-3781865 Diseases of glycosylation
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1643685 Disease
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000354955.1, ENST00000354955.2, ENST00000354955.3, ENST00000354955.4, FM, FMOD_HUMAN, NM_002023, Q06828, Q15331, Q8IV47, SLRR2E, uc317ywh.1, uc317ywh.2
UCSC ID: ENST00000354955.5_7
RefSeq Accession: NM_002023.5
Protein: Q06828 (aka FMOD_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.