Human Gene ACAN (ENST00000560601.4_7) from GENCODE V45lift37
  Description: Homo sapiens aggrecan (ACAN), transcript variant 3, mRNA. (from RefSeq NM_001369268)
RefSeq Summary (NM_001369268): This gene is a member of the aggrecan/versican proteoglycan family. The encoded protein is an integral part of the extracellular matrix in cartilagenous tissue and it withstands compression in cartilage. Mutations in this gene may be involved in skeletal dysplasia and spinal degeneration. Multiple alternatively spliced transcript variants that encode different protein isoforms have been observed in this gene. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000560601.4_7
Gencode Gene: ENSG00000157766.19_14
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 StructureGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2024-04-24 11:59:55

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

-  Comments and Description Text from UniProtKB
  ID: H0YMF1_HUMAN
DESCRIPTION: SubName: Full=Aggrecan ;
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix
SIMILARITY: Belongs to the aggrecan/versican proteoglycan family.
CAUTION: Lacks conserved residue(s) required for the propagation of feature annotation.

-  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
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-  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
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-  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
IPR001304 - C-type_lectin-like
IPR016186 - C-type_lectin-like/link_sf
IPR018378 - C-type_lectin_CS
IPR033987 - CSPG_CTLD
IPR016187 - CTDL_fold
IPR001881 - EGF-like_Ca-bd_dom
IPR000742 - EGF-like_dom
IPR000152 - EGF-type_Asp/Asn_hydroxyl_site
IPR018097 - EGF_Ca-bd_CS
IPR007110 - Ig-like_dom
IPR036179 - Ig-like_dom_sf
IPR013783 - Ig-like_fold
IPR003006 - Ig/MHC_CS
IPR003599 - Ig_sub
IPR013106 - Ig_V-set
IPR000538 - Link_dom
IPR035976 - Sushi/SCR/CCP_sf
IPR000436 - Sushi_SCR_CCP_dom

Pfam Domains:
PF00008 - EGF-like domain
PF00059 - Lectin C-type domain
PF00084 - Sushi repeat (SCR repeat)
PF07686 - Immunoglobulin V-set domain
PF00193 - Extracellular link domain

ModBase Predicted Comparative 3D Structure on H0YMF1
FrontTopSide
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0005540 hyaluronic acid binding

Biological Process:
GO:0007155 cell adhesion


-  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: ENST00000560601.1, ENST00000560601.2, ENST00000560601.3, H0YMF1, H0YMF1_HUMAN, NM_001369268, uc325ojv.1
UCSC ID: ENST00000560601.4_7
RefSeq Accession: NM_001369268
Protein: H0YMF1

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