Human Gene SMOC1 (ENST00000361956.7) Description and Page Index
  Description: Homo sapiens SPARC related modular calcium binding 1 (SMOC1), transcript variant 1, mRNA. (from RefSeq NM_001034852)
RefSeq Summary (NM_001034852): This gene encodes a multi-domain secreted protein that may have a critical role in ocular and limb development. Mutations in this gene are associated with microphthalmia and limb anomalies. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011].
Gencode Transcript: ENST00000361956.7
Gencode Gene: ENSG00000198732.10
Transcript (Including UTRs)
   Position: hg38 chr14:69,879,416-70,030,727 Size: 151,312 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg38 chr14:69,879,679-70,030,258 Size: 150,580 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:69,879,416-70,030,727)mRNA (may differ from genome)Protein (435 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
HPRDLynxMGIneXtProtOMIMPubMed
Stanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SMOC1_HUMAN
DESCRIPTION: RecName: Full=SPARC-related modular calcium-binding protein 1; AltName: Full=Secreted modular calcium-binding protein 1; Short=SMOC-1; Flags: Precursor;
FUNCTION: Plays essential roles in both eye and limb development. Probale regulator of osteoblast differentiation.
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix, basement membrane. Note=In or around the basement membrane.
TISSUE SPECIFICITY: Widely expressed in many tissues with a strongest signal in ovary. No expression in spleen.
PTM: Glycosylated.
DISEASE: Defects in SMOC1 are the cause of ophthalmoacromelic syndrome (OAS) [MIM:206920]. A rare disorder presenting with anophthalmia or microphthalmia and limb anomalies. Limb malformations include fused 4th and 5th metacarpals and short 5th finger in hands, and olygodactyly in foot (four toes). Most patients have bilateral anophthalmia/ microphthalmia, but unilateral abnormality is also noted. Other malformations are rare, but venous or vertebral anomaly was recognized each in single cases.
SIMILARITY: Contains 2 EF-hand domains.
SIMILARITY: Contains 1 Kazal-like domain.
SIMILARITY: Contains 2 thyroglobulin type-1 domains.

-  MalaCards Disease Associations
  MalaCards Gene Search: SMOC1
Diseases sorted by gene-association score: microphthalmia with limb anomalies* (1667), anophthalmos with limb anomalies* (400), microphthalmia, syndromic 9 (11), microphthalmia (10), anophthalmia/microphthalmia (9)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • D016604 Aflatoxin B1
  • D003993 Dibutyl Phthalate
  • D014212 Tretinoin
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • C016583 4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D001564 Benzo(a)pyrene
  • D019327 Copper Sulfate
  • D016572 Cyclosporine
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 31.78 RPKM in Testis
Total median expression: 346.80 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 -119.60263-0.455 Picture PostScript Text
3' UTR -138.60469-0.296 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
IPR011992 - EF-hand-like_dom
IPR018247 - EF_Hand_1_Ca_BS
IPR011497 - Kazal-type_dom
IPR002350 - Prot_inh_Kazal
IPR019577 - SPARC/Testican_Ca-bd-dom
IPR000716 - Thyroglobulin_1

Pfam Domains:
PF07648 - Kazal-type serine protease inhibitor domain
PF10591 - Secreted protein acidic and rich in cysteine Ca binding region
PF00086 - Thyroglobulin type-1 repeat

ModBase Predicted Comparative 3D Structure on Q9H4F8
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
Genome BrowserGenome BrowserNo orthologNo orthologGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGD  WormBase 
Protein SequenceProtein Sequence  Protein Sequence 
AlignmentAlignment  Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0046872 metal ion binding
GO:0050840 extracellular matrix binding

Biological Process:
GO:0001654 eye development
GO:0007165 signal transduction
GO:0007275 multicellular organism development
GO:0030154 cell differentiation
GO:0045667 regulation of osteoblast differentiation
GO:0060173 limb development

Cellular Component:
GO:0005576 extracellular region
GO:0005604 basement membrane


-  Descriptions from all associated GenBank mRNAs
  AK313063 - Homo sapiens cDNA, FLJ93541, Homo sapiens SPARC related modular calcium binding 1 (SMOC1), mRNA.
AK289988 - Homo sapiens cDNA FLJ77967 complete cds, highly similar to Homo sapiens SPARC related modular calcium binding 1, transcript variant 1, mRNA.
BC011548 - Homo sapiens SPARC related modular calcium binding 1, mRNA (cDNA clone MGC:19895 IMAGE:4549051), complete cds.
AJ249900 - Homo sapiens mRNA for secreted modular calcium-binding protein (smoc1 gene).
BC008608 - Homo sapiens SPARC related modular calcium binding 1, mRNA (cDNA clone MGC:18262 IMAGE:4158532), complete cds.
DQ894967 - Synthetic construct Homo sapiens clone IMAGE:100009427; FLH179876.01L; RZPDo839D07131D SPARC related modular calcium binding 1 (SMOC1) gene, encodes complete protein.
DQ891783 - Synthetic construct clone IMAGE:100004413; FLH179880.01X; RZPDo839D07132D SPARC related modular calcium binding 1 (SMOC1) gene, encodes complete protein.
CU679950 - Synthetic construct Homo sapiens gateway clone IMAGE:100017659 5' read SMOC1 mRNA.
KJ894527 - Synthetic construct Homo sapiens clone ccsbBroadEn_03921 SMOC1 gene, encodes complete protein.
KJ894528 - Synthetic construct Homo sapiens clone ccsbBroadEn_03922 SMOC1 gene, encodes complete protein.
JD461911 - Sequence 442935 from Patent EP1572962.
JD458247 - Sequence 439271 from Patent EP1572962.
JD187857 - Sequence 168881 from Patent EP1572962.
JD129055 - Sequence 110079 from Patent EP1572962.
JD343817 - Sequence 324841 from Patent EP1572962.
JD210359 - Sequence 191383 from Patent EP1572962.
JD437303 - Sequence 418327 from Patent EP1572962.
JD151995 - Sequence 133019 from Patent EP1572962.
JD200377 - Sequence 181401 from Patent EP1572962.
CU679003 - Synthetic construct Homo sapiens gateway clone IMAGE:100019377 5' read SMOC1 mRNA.
JD143368 - Sequence 124392 from Patent EP1572962.
JD176877 - Sequence 157901 from Patent EP1572962.
JD121054 - Sequence 102078 from Patent EP1572962.
JD343648 - Sequence 324672 from Patent EP1572962.
JD475306 - Sequence 456330 from Patent EP1572962.
JD137528 - Sequence 118552 from Patent EP1572962.
JD222023 - Sequence 203047 from Patent EP1572962.
JD083655 - Sequence 64679 from Patent EP1572962.
JD498773 - Sequence 479797 from Patent EP1572962.
AK098441 - Homo sapiens cDNA FLJ25575 fis, clone JTH07630.
JD052121 - Sequence 33145 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K1S3, B2R7P5, NM_001034852, Q96F78, Q9H4F8, SMOC1_HUMAN, uc001xlt.1, uc001xlt.2, uc001xlt.3
UCSC ID: uc001xlt.3
RefSeq Accession: NM_001034852
Protein: Q9H4F8 (aka SMOC1_HUMAN or SMO1_HUMAN)
CCDS: CCDS9798.1, CCDS32110.1

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