Human Gene COL22A1 (ENST00000303045.11_8) from GENCODE V47lift37
  Description: collagen type XXII alpha 1 chain (from RefSeq NM_152888.3)
Gencode Transcript: ENST00000303045.11_8
Gencode Gene: ENSG00000169436.18_13
Transcript (Including UTRs)
   Position: hg19 chr8:139,600,478-139,926,284 Size: 325,807 Total Exon Count: 65 Strand: -
Coding Region
   Position: hg19 chr8:139,601,496-139,895,415 Size: 293,920 Coding Exon Count: 64 

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 (chr8:139,600,478-139,926,284)mRNA (may differ from genome)Protein (1626 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: COMA1_HUMAN
DESCRIPTION: RecName: Full=Collagen alpha-1(XXII) chain; Flags: Precursor;
FUNCTION: Acts as a cell adhesion ligand for skin epithelial cells and fibroblasts.
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix. Cytoplasm (By similarity).
TISSUE SPECIFICITY: Restrictive expression is observed at tissue junctions such as the myotendinous junction in skeletal and heart muscle, the articular cartilage-synovial fluid junction, or the border between the anagen hair follicle and the dermis in the skin. It is deposited in the basement membrane zone of the myotendinous junction and the hair follicle and associated with the extrafibrillar matrix in cartilage.
SIMILARITY: Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
SIMILARITY: Contains 16 collagen-like domains.
SIMILARITY: Contains 1 laminin G-like domain.
SIMILARITY: Contains 1 VWFA 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: COL22A1
Diseases sorted by gene-association score: diffuse cutaneous systemic sclerosis (2)

-  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: 65.58 RPKM in Pituitary
Total median expression: 82.87 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 -184.30495-0.372 Picture PostScript Text
3' UTR -283.501018-0.278 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
IPR008160 - Collagen
IPR008985 - ConA-like_lec_gl_sf
IPR001791 - Laminin_G
IPR002035 - VWF_A

Pfam Domains:
PF00092 - von Willebrand factor type A domain
PF01391 - Collagen triple helix repeat (20 copies)
PF13519 - von Willebrand factor type A domain

SCOP Domains:
49899 - Concanavalin A-like lectins/glucanases
53300 - vWA-like

ModBase Predicted Comparative 3D Structure on Q8NFW1
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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
  Cellular Component:
GO:0005576 extracellular region
GO:0005581 collagen trimer
GO:0005737 cytoplasm
GO:0005788 endoplasmic reticulum lumen


-  Descriptions from all associated GenBank mRNAs
  AF406780 - Homo sapiens alpha 1 type XXII collagen mRNA, complete cds.
BC042075 - Homo sapiens collagen, type XXII, alpha 1, mRNA (cDNA clone IMAGE:5742944), partial cds.
BC144535 - Homo sapiens collagen, type XXII, alpha 1, mRNA (cDNA clone MGC:178079 IMAGE:9053062), complete cds.
BC172420 - Synthetic construct Homo sapiens clone IMAGE:100069114, MGC:199125 collagen, type XXII, alpha 1 (COL22A1) mRNA, encodes complete protein.
JD354408 - Sequence 335432 from Patent EP1572962.
JD233347 - Sequence 214371 from Patent EP1572962.
AX721208 - Sequence 168 from Patent WO0220754.
JD455542 - Sequence 436566 from Patent EP1572962.
JD179018 - Sequence 160042 from Patent EP1572962.
JD126819 - Sequence 107843 from Patent EP1572962.
JD434714 - Sequence 415738 from Patent EP1572962.
JD309596 - Sequence 290620 from Patent EP1572962.
JD037787 - Sequence 18811 from Patent EP1572962.
JD066365 - Sequence 47389 from Patent EP1572962.
JD042270 - Sequence 23294 from Patent EP1572962.
JD483312 - Sequence 464336 from Patent EP1572962.
JD468744 - Sequence 449768 from Patent EP1572962.
JD298489 - Sequence 279513 from Patent EP1572962.
JD202902 - Sequence 183926 from Patent EP1572962.
JD230563 - Sequence 211587 from Patent EP1572962.
JD310422 - Sequence 291446 from Patent EP1572962.
JD040080 - Sequence 21104 from Patent EP1572962.
JD424421 - Sequence 405445 from Patent EP1572962.
JD071634 - Sequence 52658 from Patent EP1572962.
JD264359 - Sequence 245383 from Patent EP1572962.
JD495427 - Sequence 476451 from Patent EP1572962.
JD507604 - Sequence 488628 from Patent EP1572962.
JD519511 - Sequence 500535 from Patent EP1572962.
JD327566 - Sequence 308590 from Patent EP1572962.
JD555139 - Sequence 536163 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8NFW1 (Reactome details) participates in the following event(s):

R-HSA-8944227 Association of procollagen type XXII
R-HSA-2002460 P4HB binds Collagen chains
R-HSA-8948230 P3HB binds 4-Hyp-collagen propeptides
R-HSA-8944246 Association of procollagen type XXI
R-HSA-1650808 Prolyl 4-hydroxylase converts collagen prolines to 4-hydroxyprolines
R-HSA-1980233 Collagen prolyl 3-hydroxylase converts 4-Hyp collagen to 3,4-Hyp collagen
R-HSA-8948219 PLOD3 binds Lysyl hydroxylated collagen propeptides
R-HSA-8948228 COLGALT1,COLGALT2 bind Lysyl hydroxylated collagen propeptides
R-HSA-2022073 Procollagen triple helix formation
R-HSA-1981104 Procollagen lysyl hydroxylases convert collagen lysines to 5-hydroxylysines
R-HSA-1981120 Galactosylation of collagen propeptide hydroxylysines by procollagen galactosyltransferases 1, 2.
R-HSA-1981128 Galactosylation of collagen propeptide hydroxylysines by PLOD3
R-HSA-1981157 Glucosylation of collagen propeptide hydroxylysines
R-HSA-8948216 Collagen chain trimerization
R-HSA-1650814 Collagen biosynthesis and modifying enzymes
R-HSA-1474290 Collagen formation
R-HSA-1474244 Extracellular matrix organization

-  Other Names for This Gene
  Alternate Gene Symbols: B7ZMH0, C9K0G4, COMA1_HUMAN, ENST00000303045.1, ENST00000303045.10, ENST00000303045.2, ENST00000303045.3, ENST00000303045.4, ENST00000303045.5, ENST00000303045.6, ENST00000303045.7, ENST00000303045.8, ENST00000303045.9, NM_152888, Q8IVT9, Q8NFW1, uc317ndz.1, uc317ndz.2
UCSC ID: ENST00000303045.11_8
RefSeq Accession: NM_152888.3
Protein: Q8NFW1 (aka COMA1_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.