Mouse Gene Col26a1 (ENSMUST00000111103.1) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus collagen, type XXVI, alpha 1 (Col26a1), transcript variant 2, mRNA. (from RefSeq NM_001346699)
Gencode Transcript: ENSMUST00000111103.1
Gencode Gene: ENSMUSG00000004415.15
Transcript (Including UTRs)
   Position: mm10 chr5:136,741,759-136,883,184 Size: 141,426 Total Exon Count: 13 Strand: -
Coding Region
   Position: mm10 chr5:136,743,046-136,883,007 Size: 139,962 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:136,741,759-136,883,184)mRNA (may differ from genome)Protein (438 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: EMID2_MOUSE
DESCRIPTION: RecName: Full=Collagen alpha-1(XXVI) chain; AltName: Full=EMI domain-containing protein 2; AltName: Full=Emilin and multimerin domain-containing protein 2; Short=Emu2; Flags: Precursor;
SUBUNIT: Homotrimer or heterotrimer.
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix.
TISSUE SPECIFICITY: Specifically expressed in the testis and ovary in adult tissues.
DEVELOPMENTAL STAGE: At E9.5 it is expressed in the somites and in mesenchymal cells of the head and the branchial arches. At E14.5 it is expressed in the surrounding mesenchyme of the kidney and the inner ear. Expression is also observed in the spinal nerves and ganglia, the mesenchyme of the skull, the diaphragm, and the skeletal muscles.
PTM: Hydroxylated on proline residues.
PTM: N-glycosylated.
SIMILARITY: Contains 2 collagen-like domains.
SIMILARITY: Contains 1 EMI 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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -68.90177-0.389 Picture PostScript Text
3' UTR -511.301287-0.397 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
IPR011489 - EMI_domain

Pfam Domains:
PF01391 - Collagen triple helix repeat (20 copies)
PF07546 - EMI domain

ModBase Predicted Comparative 3D Structure on Q91VF6
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0010811 positive regulation of cell-substrate adhesion

Cellular Component:
GO:0005576 extracellular region
GO:0005581 collagen trimer
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus


-  Descriptions from all associated GenBank mRNAs
  BC075713 - Mus musculus EMI domain containing 2, mRNA (cDNA clone MGC:78097 IMAGE:6313353), complete cds.
AK143515 - Mus musculus 12 days embryo whole body cDNA, RIKEN full-length enriched library, clone:E970001O18 product:EMI domain containing 2, full insert sequence.
AJ416092 - Mus musculus mRNA for putative emu2 protein.
AK076445 - Mus musculus 0 day neonate head cDNA, RIKEN full-length enriched library, clone:4832437G21 product:Emu2 gene, full insert sequence.
AK133882 - Mus musculus 8 days embryo whole body cDNA, RIKEN full-length enriched library, clone:5730485L17 product:EMI domain containing 2, full insert sequence.
AB085837 - Mus musculus mRNA for type XXVI collagen, complete cds.
AK051600 - Mus musculus 12 days embryo spinal ganglion cDNA, RIKEN full-length enriched library, clone:D130059G12 product:Emu2 gene, full insert sequence.
AK079128 - Mus musculus 12 days embryo embryonic body between diaphragm region and neck cDNA, RIKEN full-length enriched library, clone:9430032K24 product:EMI domain containing 2, full insert sequence.
BC002218 - Mus musculus EMI domain containing 2, mRNA (cDNA clone IMAGE:3490530), complete cds.
AK089137 - Mus musculus 10 days neonate olfactory brain cDNA, RIKEN full-length enriched library, clone:E530013F23 product:EMI domain containing 2, full insert sequence.

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

Protein Q91VF6 (Reactome details) participates in the following event(s):

R-MMU-8944250 Association of procollagen type XXV
R-MMU-8944254 Association of procollagen type XXVI
R-MMU-2002460 P4HB binds Collagen chains
R-MMU-8948230 P3HB binds 4-Hyp-collagen propeptides
R-MMU-1650808 Prolyl 4-hydroxylase converts collagen prolines to 4-hydroxyprolines
R-MMU-1980233 Collagen prolyl 3-hydroxylase converts 4-Hyp collagen to 3,4-Hyp collagen
R-MMU-8948219 PLOD3 binds Lysyl hydroxylated collagen propeptides
R-MMU-8948228 COLGALT1,COLGALT2 bind Lysyl hydroxylated collagen propeptides
R-MMU-2471842 Collagen type XXV ectomain shedding
R-MMU-2022073 Procollagen triple helix formation
R-MMU-1981104 Procollagen lysyl hydroxylases convert collagen lysines to 5-hydroxylysines
R-MMU-1981120 Galactosylation of collagen propeptide hydroxylysines by procollagen galactosyltransferases 1, 2.
R-MMU-1981128 Galactosylation of collagen propeptide hydroxylysines by PLOD3
R-MMU-1981157 Glucosylation of collagen propeptide hydroxylysines
R-MMU-8948216 Collagen chain trimerization
R-MMU-1650814 Collagen biosynthesis and modifying enzymes
R-MMU-1474290 Collagen formation
R-MMU-1442490 Collagen degradation
R-MMU-1474244 Extracellular matrix organization
R-MMU-1474228 Degradation of the extracellular matrix

-  Other Names for This Gene
  Alternate Gene Symbols: Col26a, Emid2, EMID2_MOUSE, Emu2, NM_001346699, Q8K4P3, Q91VF6, uc009aaz.1, uc009aaz.2
UCSC ID: uc009aaz.2
RefSeq Accession: NM_001346699
Protein: Q91VF6 (aka EMID2_MOUSE or EMD2_MOUSE)
CCDS: CCDS19755.1, CCDS84976.1

-  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.