Human Gene COL4A6 (ENST00000477085.1) from GENCODE V44
  Description: collagen type IV alpha 6 chain (from HGNC COL4A6)
RefSeq Summary (NM_001847): This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene, alpha 5 type IV collagen, so that the gene pair shares a common promoter. Deletions in the alpha 5 gene that extend into the alpha 6 gene result in diffuse leiomyomatosis accompanying the X-linked Alport syndrome caused by the deletion in the alpha 5 gene. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2013].
Gencode Transcript: ENST00000477085.1
Gencode Gene: ENSG00000197565.17
Transcript (Including UTRs)
   Position: hg38 chrX:108,267,642-108,439,497 Size: 171,856 Total Exon Count: 4 Strand: -


Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionOther SpeciesmRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:108,267,642-108,439,497)mRNA (may differ from genome)No protein
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
EnsemblExonPrimerGencodeHGNCLynxMalacards
PubMedWikipedia

-  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: COL4A6
Diseases sorted by gene-association score: deafness, x-linked 6* (1279), dfnx6 nonsyndromic hearing loss and deafness* (500), x-linked non-syndromic sensorineural deafness type dfn* (202), leiomyomatosis (42), alport syndrome (40), x-linked diffuse leiomyomatosis-alport syndrome* (25), leiomyoma (12), alport syndrome, autosomal recessive (8)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 73.51 RPKM in Esophagus - Muscularis
Total median expression: 250.41 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.

-  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
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  D21337 - Homo sapiens mRNA for collagen, complete cds.
BC140855 - Homo sapiens collagen, type IV, alpha 6, mRNA (cDNA clone MGC:176532 IMAGE:9021723), complete cds.
BC144669 - Homo sapiens collagen, type IV, alpha 6, mRNA (cDNA clone MGC:178217 IMAGE:9053200), complete cds.
U04845 - Homo sapiens A type IV collagen (COL4A6) mRNA, complete cds.
L22763 - Human alpha-6 type IV collagen mRNA, 5' end.
BC000874 - Homo sapiens, Similar to collagen, type IV, alpha 6, clone IMAGE:3461295, mRNA.
BC070203 - Homo sapiens collagen, type IV, alpha 6, mRNA (cDNA clone IMAGE:4274195), complete cds.
BC005305 - Homo sapiens collagen, type IV, alpha 6, mRNA (cDNA clone IMAGE:3951220), complete cds.
KJ901346 - Synthetic construct Homo sapiens clone ccsbBroadEn_10740 COL4A6 gene, encodes complete protein.
BT007228 - Homo sapiens collagen, type IV, alpha 6 mRNA, complete cds.
JD200623 - Sequence 181647 from Patent EP1572962.
JD488484 - Sequence 469508 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04510 - Focal adhesion
hsa04512 - ECM-receptor interaction
hsa05200 - Pathways in cancer
hsa05222 - Small cell lung cancer

BioCarta from NCI Cancer Genome Anatomy Project
h_amiPathway - Acute Myocardial Infarction
h_plateletAppPathway - Platelet Amyloid Precursor Protein Pathway
h_intrinsicPathway - Intrinsic Prothrombin Activation Pathway
h_npp1Pathway - Regulators of Bone Mineralization
h_ace2Pathway - Angiotensin-converting enzyme 2 regulates heart function
h_vitCBPathway - Vitamin C in the Brain

-  Other Names for This Gene
  Alternate Gene Symbols: BC005305, uc004eny.1, uc004eny.2, uc004eny.3
UCSC ID: ENST00000477085.1
RefSeq Accession: NM_001847

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