Mouse Gene Col6a3 (ENSMUST00000188587.6) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Col6a3 (from geneSymbol)
Gencode Transcript: ENSMUST00000188587.6
Gencode Gene: ENSMUSG00000048126.16
Transcript (Including UTRs)
   Position: mm10 chr1:90,765,923-90,843,971 Size: 78,049 Total Exon Count: 41 Strand: -
Coding Region
   Position: mm10 chr1:90,765,923-90,830,230 Size: 64,308 Coding Exon Count: 40 

Page IndexSequence and LinksPrimersCTDRNA StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2019-09-20

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:90,765,923-90,843,971)mRNA (may differ from genome)Protein (2677 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsPubMedSOURCE
UniProtKBWikipedia

-  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
  • D000082 Acetaminophen
  • D001564 Benzo(a)pyrene
  • D003907 Dexamethasone
  • D004317 Doxorubicin
  • D013629 Tamoxifen
  • C070379 1,2-bis(2-aminophenoxy)ethane N,N,N',N'-tetraacetic acid acetoxymethyl ester
  • D015056 1-Methyl-3-isobutylxanthine
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • D015124 8-Bromo Cyclic Adenosine Monophosphate
  • C547126 AZM551248
          more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -82.30254-0.324 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.

-  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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  LF192788 - JP 2014500723-A/291: Polycomb-Associated Non-Coding RNAs.
AF064749 - Mus musculus type VI collagen alpha 3 subunit mRNA, complete cds.
AF034136 - Mus musculus collagen alpha3(VI) (Col6a3) mRNA, partial cds.
MA428365 - JP 2018138019-A/291: Polycomb-Associated Non-Coding RNAs.
BC080662 - Mus musculus collagen, type VI, alpha 3, mRNA (cDNA clone IMAGE:4483085), partial cds.
BC057903 - Mus musculus collagen, type VI, alpha 3, mRNA (cDNA clone IMAGE:5025735), complete cds.
BC049881 - Mus musculus collagen, type VI, alpha 3, mRNA (cDNA clone IMAGE:5253759), complete cds.
BC005491 - Mus musculus collagen, type VI, alpha 3, mRNA (cDNA clone IMAGE:3486796), partial cds.
LF217008 - JP 2014500723-A/24511: Polycomb-Associated Non-Coding RNAs.
LF217011 - JP 2014500723-A/24514: Polycomb-Associated Non-Coding RNAs.
LF217013 - JP 2014500723-A/24516: Polycomb-Associated Non-Coding RNAs.
LF217016 - JP 2014500723-A/24519: Polycomb-Associated Non-Coding RNAs.
LF217019 - JP 2014500723-A/24522: Polycomb-Associated Non-Coding RNAs.
LF217021 - JP 2014500723-A/24524: Polycomb-Associated Non-Coding RNAs.
LF217023 - JP 2014500723-A/24526: Polycomb-Associated Non-Coding RNAs.
LF217024 - JP 2014500723-A/24527: Polycomb-Associated Non-Coding RNAs.
Z18279 - Mus musculus collagen alpha 3 chain type VI.
LF217025 - JP 2014500723-A/24528: Polycomb-Associated Non-Coding RNAs.
LF217026 - JP 2014500723-A/24529: Polycomb-Associated Non-Coding RNAs.
LF217027 - JP 2014500723-A/24530: Polycomb-Associated Non-Coding RNAs.
LF217028 - JP 2014500723-A/24531: Polycomb-Associated Non-Coding RNAs.
LF217030 - JP 2014500723-A/24533: Polycomb-Associated Non-Coding RNAs.
LF217032 - JP 2014500723-A/24535: Polycomb-Associated Non-Coding RNAs.
LF217034 - JP 2014500723-A/24537: Polycomb-Associated Non-Coding RNAs.
LF217036 - JP 2014500723-A/24539: Polycomb-Associated Non-Coding RNAs.
LF217037 - JP 2014500723-A/24540: Polycomb-Associated Non-Coding RNAs.
LF217038 - JP 2014500723-A/24541: Polycomb-Associated Non-Coding RNAs.
LF217040 - JP 2014500723-A/24543: Polycomb-Associated Non-Coding RNAs.
LF217041 - JP 2014500723-A/24544: Polycomb-Associated Non-Coding RNAs.
AK076391 - Mus musculus 10 days neonate skin cDNA, RIKEN full-length enriched library, clone:4732489C18 product:procollagen, type VI, alpha 3, full insert sequence.
LF217044 - JP 2014500723-A/24547: Polycomb-Associated Non-Coding RNAs.
LF217045 - JP 2014500723-A/24548: Polycomb-Associated Non-Coding RNAs.
LF217046 - JP 2014500723-A/24549: Polycomb-Associated Non-Coding RNAs.
LF217048 - JP 2014500723-A/24551: Polycomb-Associated Non-Coding RNAs.
LF217050 - JP 2014500723-A/24553: Polycomb-Associated Non-Coding RNAs.
LF217052 - JP 2014500723-A/24555: Polycomb-Associated Non-Coding RNAs.
LF217055 - JP 2014500723-A/24558: Polycomb-Associated Non-Coding RNAs.
LF217057 - JP 2014500723-A/24560: Polycomb-Associated Non-Coding RNAs.
LF217061 - JP 2014500723-A/24564: Polycomb-Associated Non-Coding RNAs.
LF217062 - JP 2014500723-A/24565: Polycomb-Associated Non-Coding RNAs.
LF217064 - JP 2014500723-A/24567: Polycomb-Associated Non-Coding RNAs.
LF217065 - JP 2014500723-A/24568: Polycomb-Associated Non-Coding RNAs.
LF217066 - JP 2014500723-A/24569: Polycomb-Associated Non-Coding RNAs.
LF217067 - JP 2014500723-A/24570: Polycomb-Associated Non-Coding RNAs.
LF217068 - JP 2014500723-A/24571: Polycomb-Associated Non-Coding RNAs.
LF217069 - JP 2014500723-A/24572: Polycomb-Associated Non-Coding RNAs.
LF217071 - JP 2014500723-A/24574: Polycomb-Associated Non-Coding RNAs.
LF217072 - JP 2014500723-A/24575: Polycomb-Associated Non-Coding RNAs.
LF217074 - JP 2014500723-A/24577: Polycomb-Associated Non-Coding RNAs.
LF217076 - JP 2014500723-A/24579: Polycomb-Associated Non-Coding RNAs.
LF217077 - JP 2014500723-A/24580: Polycomb-Associated Non-Coding RNAs.
LF217078 - JP 2014500723-A/24581: Polycomb-Associated Non-Coding RNAs.
LF217080 - JP 2014500723-A/24583: Polycomb-Associated Non-Coding RNAs.
LF217081 - JP 2014500723-A/24584: Polycomb-Associated Non-Coding RNAs.
LF217082 - JP 2014500723-A/24585: Polycomb-Associated Non-Coding RNAs.
LF217083 - JP 2014500723-A/24586: Polycomb-Associated Non-Coding RNAs.
LF217084 - JP 2014500723-A/24587: Polycomb-Associated Non-Coding RNAs.
LF217086 - JP 2014500723-A/24589: Polycomb-Associated Non-Coding RNAs.
LF217087 - JP 2014500723-A/24590: Polycomb-Associated Non-Coding RNAs.
LF217089 - JP 2014500723-A/24592: Polycomb-Associated Non-Coding RNAs.
LF217095 - JP 2014500723-A/24598: Polycomb-Associated Non-Coding RNAs.
LF217097 - JP 2014500723-A/24600: Polycomb-Associated Non-Coding RNAs.
MA452585 - JP 2018138019-A/24511: Polycomb-Associated Non-Coding RNAs.
MA452588 - JP 2018138019-A/24514: Polycomb-Associated Non-Coding RNAs.
MA452590 - JP 2018138019-A/24516: Polycomb-Associated Non-Coding RNAs.
MA452593 - JP 2018138019-A/24519: Polycomb-Associated Non-Coding RNAs.
MA452596 - JP 2018138019-A/24522: Polycomb-Associated Non-Coding RNAs.
MA452598 - JP 2018138019-A/24524: Polycomb-Associated Non-Coding RNAs.
MA452600 - JP 2018138019-A/24526: Polycomb-Associated Non-Coding RNAs.
MA452601 - JP 2018138019-A/24527: Polycomb-Associated Non-Coding RNAs.
MA452602 - JP 2018138019-A/24528: Polycomb-Associated Non-Coding RNAs.
MA452603 - JP 2018138019-A/24529: Polycomb-Associated Non-Coding RNAs.
MA452604 - JP 2018138019-A/24530: Polycomb-Associated Non-Coding RNAs.
MA452605 - JP 2018138019-A/24531: Polycomb-Associated Non-Coding RNAs.
MA452607 - JP 2018138019-A/24533: Polycomb-Associated Non-Coding RNAs.
MA452609 - JP 2018138019-A/24535: Polycomb-Associated Non-Coding RNAs.
MA452611 - JP 2018138019-A/24537: Polycomb-Associated Non-Coding RNAs.
MA452613 - JP 2018138019-A/24539: Polycomb-Associated Non-Coding RNAs.
MA452614 - JP 2018138019-A/24540: Polycomb-Associated Non-Coding RNAs.
MA452615 - JP 2018138019-A/24541: Polycomb-Associated Non-Coding RNAs.
MA452617 - JP 2018138019-A/24543: Polycomb-Associated Non-Coding RNAs.
MA452618 - JP 2018138019-A/24544: Polycomb-Associated Non-Coding RNAs.
MA452621 - JP 2018138019-A/24547: Polycomb-Associated Non-Coding RNAs.
MA452622 - JP 2018138019-A/24548: Polycomb-Associated Non-Coding RNAs.
MA452623 - JP 2018138019-A/24549: Polycomb-Associated Non-Coding RNAs.
MA452625 - JP 2018138019-A/24551: Polycomb-Associated Non-Coding RNAs.
MA452627 - JP 2018138019-A/24553: Polycomb-Associated Non-Coding RNAs.
MA452629 - JP 2018138019-A/24555: Polycomb-Associated Non-Coding RNAs.
MA452632 - JP 2018138019-A/24558: Polycomb-Associated Non-Coding RNAs.
MA452634 - JP 2018138019-A/24560: Polycomb-Associated Non-Coding RNAs.
MA452638 - JP 2018138019-A/24564: Polycomb-Associated Non-Coding RNAs.
MA452639 - JP 2018138019-A/24565: Polycomb-Associated Non-Coding RNAs.
MA452641 - JP 2018138019-A/24567: Polycomb-Associated Non-Coding RNAs.
MA452642 - JP 2018138019-A/24568: Polycomb-Associated Non-Coding RNAs.
MA452643 - JP 2018138019-A/24569: Polycomb-Associated Non-Coding RNAs.
MA452644 - JP 2018138019-A/24570: Polycomb-Associated Non-Coding RNAs.
MA452645 - JP 2018138019-A/24571: Polycomb-Associated Non-Coding RNAs.
MA452646 - JP 2018138019-A/24572: Polycomb-Associated Non-Coding RNAs.
MA452648 - JP 2018138019-A/24574: Polycomb-Associated Non-Coding RNAs.
MA452649 - JP 2018138019-A/24575: Polycomb-Associated Non-Coding RNAs.
MA452651 - JP 2018138019-A/24577: Polycomb-Associated Non-Coding RNAs.
MA452653 - JP 2018138019-A/24579: Polycomb-Associated Non-Coding RNAs.
MA452654 - JP 2018138019-A/24580: Polycomb-Associated Non-Coding RNAs.
MA452655 - JP 2018138019-A/24581: Polycomb-Associated Non-Coding RNAs.
MA452657 - JP 2018138019-A/24583: Polycomb-Associated Non-Coding RNAs.
MA452658 - JP 2018138019-A/24584: Polycomb-Associated Non-Coding RNAs.
MA452659 - JP 2018138019-A/24585: Polycomb-Associated Non-Coding RNAs.
MA452660 - JP 2018138019-A/24586: Polycomb-Associated Non-Coding RNAs.
MA452661 - JP 2018138019-A/24587: Polycomb-Associated Non-Coding RNAs.
MA452663 - JP 2018138019-A/24589: Polycomb-Associated Non-Coding RNAs.
MA452664 - JP 2018138019-A/24590: Polycomb-Associated Non-Coding RNAs.
MA452666 - JP 2018138019-A/24592: Polycomb-Associated Non-Coding RNAs.
MA452672 - JP 2018138019-A/24598: Polycomb-Associated Non-Coding RNAs.
MA452674 - JP 2018138019-A/24600: Polycomb-Associated Non-Coding RNAs.
LF217111 - JP 2014500723-A/24614: Polycomb-Associated Non-Coding RNAs.
LF217113 - JP 2014500723-A/24616: Polycomb-Associated Non-Coding RNAs.
MA452688 - JP 2018138019-A/24614: Polycomb-Associated Non-Coding RNAs.
MA452690 - JP 2018138019-A/24616: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu04510 - Focal adhesion
mmu04512 - ECM-receptor interaction
mmu04974 - Protein digestion and absorption

-  Other Names for This Gene
  Alternate Gene Symbols: A0A087WS16, AF064749, uc287kih.1
UCSC ID: uc287kih.1
RefSeq Accession: NM_001243009
CCDS: CCDS56640.1

-  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.