Human Gene ACAN (ENST00000560601.4_8) from GENCODE V47lift37
  Description: aggrecan, transcript variant 3 (from RefSeq NM_001369268.1)
Gencode Transcript: ENST00000560601.4_8
Gencode Gene: ENSG00000157766.19_15
Transcript (Including UTRs)
   Position: hg19 chr15:89,346,667-89,418,584 Size: 71,918 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg19 chr15:89,379,438-89,417,712 Size: 38,275 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:89,346,667-89,418,584)mRNA (may differ from genome)Protein (2568 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: H0YMF1_HUMAN
DESCRIPTION: SubName: Full=Aggrecan core protein; Flags: Fragment;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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: ACAN
Diseases sorted by gene-association score: spondyloepimetaphyseal dysplasia, aggrecan type* (1729), osteochondritis dissecans, short stature, and early-onset osteoarthritis* (1681), spondyloepiphyseal dysplasia, kimberley type* (1350), osteochondritis dissecans* (446), short stature-advanced bone age-early-onset osteoarthritis syndrome* (350), osteoarthritis (48), degenerative disc disease (27), familial osteochondritis dissecans (18), skeletal dysplasia (13), bone deterioration disease (13), bone structure disease (13), spinal stenosis (13), pseudoachondroplasia (12), achondroplasia (12), spondyloepimetaphyseal dysplasia (11), multiple epiphyseal dysplasia (10), spondyloepiphyseal dysplasia with congenital joint dislocations (10), exotropia (8), achondrogenesis, type ia (8), hutchinson-gilford progeria (7), idiopathic scoliosis (7), cleidocranial dysplasia (7), bone inflammation disease (6), cartilage disease (6), arthropathy (6), chondroid chordoma (5), transient arthritis (5), odontogenic myxoma (5), ischemic bone disease (5), achondrogenesis, type ii or hypochondrogenesis (5), arthritis (5), polyradiculopathy (5), hypochondrogenesis (4)
* = 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: 11.89 RPKM in Artery - Tibial
Total median expression: 26.49 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 -174.70381-0.459 Picture PostScript Text
3' UTR -311.60872-0.357 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
IPR016186 - C-type_lectin-like
IPR016187 - C-type_lectin_fold
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

Pfam Domains:
PF00008 - EGF-like domain
PF00059 - Lectin C-type domain
PF00084 - Sushi repeat (SCR repeat)
PF00193 - Extracellular link domain
PF07645 - Calcium-binding EGF domain
PF07686 - Immunoglobulin V-set domain
PF12661 - Human growth factor-like EGF

SCOP Domains:
48726 - Immunoglobulin
56436 - C-type lectin-like
57535 - Complement control module/SCR domain
57196 - EGF/Laminin
57184 - Growth factor receptor domain

ModBase Predicted Comparative 3D Structure on H0YMF1
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    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding


-  Descriptions from all associated GenBank mRNAs
  AK290723 - Homo sapiens cDNA FLJ77079 complete cds, highly similar to Homo sapiens aggrecan 1 (chondroitin sulfate proteoglycan 1, large aggregating proteoglycan, antigen identified by monoclonal antibody A0122), mRNA.
BC036445 - Homo sapiens aggrecan, mRNA (cDNA clone IMAGE:4823544), complete cds.
BC150624 - Homo sapiens aggrecan, mRNA (cDNA clone MGC:183534 IMAGE:9056994), complete cds.
M55172 - Human large aggregating cartilage proteoglycan core protein mRNA, complete cds.
U13192 - Human aggrecan mRNA, 5' UTR including exon 1.
JD312722 - Sequence 293746 from Patent EP1572962.
JD078875 - Sequence 59899 from Patent EP1572962.
X80278 - H.sapiens aggrecan mRNA.
X17406 - Human mRNA for cartilage specific proteoglycan.
J05062 - Human cartilage-specific proteoglycan core protein (CSPCP) mRNA, 3' end.
L12234 - Human aggrecan mRNA, exon 1.
JD140736 - Sequence 121760 from Patent EP1572962.
JD199310 - Sequence 180334 from Patent EP1572962.
JD119236 - Sequence 100260 from Patent EP1572962.
JD111433 - Sequence 92457 from Patent EP1572962.
MP012943 - Sequence 3 from Patent EP3397294.

-  Other Names for This Gene
  Alternate Gene Symbols: ACAN , ENST00000560601.1, ENST00000560601.2, ENST00000560601.3, H0YMF1, H0YMF1_HUMAN, NM_001369268, uc325ojv.1, uc325ojv.2
UCSC ID: ENST00000560601.4_8
RefSeq Accession: NM_001369268.1
Protein: H0YMF1

-  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.