Human Gene ECM2 (ENST00000344604.10_9) from GENCODE V47lift37
  Description: extracellular matrix protein 2, transcript variant 1 (from RefSeq NM_001393.4)
Gencode Transcript: ENST00000344604.10_9
Gencode Gene: ENSG00000106823.13_16
Transcript (Including UTRs)
   Position: hg19 chr9:95,257,597-95,298,272 Size: 40,676 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr9:95,258,597-95,285,148 Size: 26,552 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:95,257,597-95,298,272)mRNA (may differ from genome)Protein (699 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ECM2_HUMAN
DESCRIPTION: RecName: Full=Extracellular matrix protein 2; AltName: Full=Matrix glycoprotein SC1/ECM2; Flags: Precursor;
FUNCTION: Promotes matrix assembly and cell adhesiveness (By similarity).
SUBUNIT: Interacts with numerous extracellular matrix proteins (By similarity).
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix.
TISSUE SPECIFICITY: Expressed predominantly in adipose tissue as well as female-specific organs such as mammary gland, ovary, and uterus.
SIMILARITY: Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class I subfamily.
SIMILARITY: Contains 13 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 LRRNT domain.
SIMILARITY: Contains 1 VWFC domain.
SEQUENCE CAUTION: Sequence=CAD97940.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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


-  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: 29.20 RPKM in Artery - Coronary
Total median expression: 293.46 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 -15.2085-0.179 Picture PostScript Text
3' UTR -184.801000-0.185 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
IPR001007 - VWF_C

Pfam Domains:
PF00093 - von Willebrand factor type C domain
PF13306 - BspA type Leucine rich repeat region (6 copies)
PF13516 - Leucine Rich repeat
PF13855 - Leucine rich repeat

SCOP Domains:
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1
57603 - FnI-like domain

ModBase Predicted Comparative 3D Structure on O94769
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     
  Ensembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005178 integrin binding
GO:0005518 collagen binding
GO:0008201 heparin binding
GO:0070052 collagen V binding

Biological Process:
GO:0007160 cell-matrix adhesion
GO:0010811 positive regulation of cell-substrate adhesion
GO:0030198 extracellular matrix organization
GO:0007409 axonogenesis

Cellular Component:
GO:0005576 extracellular region
GO:0005614 interstitial matrix
GO:0005615 extracellular space
GO:0031012 extracellular matrix


-  Descriptions from all associated GenBank mRNAs
  BX537976 - Homo sapiens mRNA; cDNA DKFZp686O0186 (from clone DKFZp686O0186); complete cds.
AB011792 - Homo sapiens mRNA for extracellular matrix protein, complete cds.
AK303922 - Homo sapiens cDNA FLJ51183 complete cds, highly similar to Extracellular matrix protein 2 precursor.
AK298278 - Homo sapiens cDNA FLJ51022 complete cds, highly similar to Extracellular matrix protein 2 precursor.
AK296458 - Homo sapiens cDNA FLJ51676 complete cds, highly similar to Extracellular matrix protein 2 precursor.
AK312820 - Homo sapiens cDNA, FLJ93257, Homo sapiens extracellular matrix protein 2, female organ andadipocyte specific (ECM2), mRNA.
AB527312 - Synthetic construct DNA, clone: pF1KE0009, Homo sapiens ECM2 gene for extracellular matrix protein 2, female organ and adipocyte specific, without stop codon, in Flexi system.
AM393123 - Synthetic construct Homo sapiens clone IMAGE:100001929 for hypothetical protein (ECM2 gene).
JD545746 - Sequence 526770 from Patent EP1572962.
AK308485 - Homo sapiens cDNA, FLJ98526.
BC105958 - Homo sapiens extracellular matrix protein 2, female organ and adipocyte specific, mRNA (cDNA clone MGC:126355 IMAGE:40035034), complete cds.
BC107493 - Homo sapiens extracellular matrix protein 2, female organ and adipocyte specific, mRNA (cDNA clone MGC:126356 IMAGE:40035036), complete cds.
JD313548 - Sequence 294572 from Patent EP1572962.
JD341132 - Sequence 322156 from Patent EP1572962.
JD434754 - Sequence 415778 from Patent EP1572962.
JD038130 - Sequence 19154 from Patent EP1572962.
JD486688 - Sequence 467712 from Patent EP1572962.
JD284054 - Sequence 265078 from Patent EP1572962.
JD291353 - Sequence 272377 from Patent EP1572962.
BC036806 - Homo sapiens extracellular matrix protein 2, female organ and adipocyte specific, mRNA (cDNA clone IMAGE:5725929), partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: B2R730, E2PU11, ECM2_HUMAN, ENST00000344604.1, ENST00000344604.2, ENST00000344604.3, ENST00000344604.4, ENST00000344604.5, ENST00000344604.6, ENST00000344604.7, ENST00000344604.8, ENST00000344604.9, NM_001393, O94769, Q5T9F2, Q7Z3D0, uc317wzp.1, uc317wzp.2
UCSC ID: ENST00000344604.10_9
RefSeq Accession: NM_001393.4
Protein: O94769 (aka ECM2_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.