Human Gene UBIAD1 (uc001asg.3) Description and Page Index
  Description: Homo sapiens UbiA prenyltransferase domain containing 1 (UBIAD1), mRNA.
RefSeq Summary (NM_013319): This gene encodes a protein thought to be involved in cholesterol and phospholipid metabolism. Mutations in this gene are associated with Schnyder crystalline corneal dystrophy. [provided by RefSeq, Oct 2008].
Transcript (Including UTRs)
   Position: hg19 chr1:11,333,255-11,348,491 Size: 15,237 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr1:11,333,589-11,346,188 Size: 12,600 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:11,333,255-11,348,491)mRNA (may differ from genome)Protein (338 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: UBIA1_HUMAN
DESCRIPTION: RecName: Full=UbiA prenyltransferase domain-containing protein 1; EC=2.5.1.-; AltName: Full=Transitional epithelial response protein 1;
FUNCTION: Prenyltransferase that mediates the formation of menaquinone-4 (MK-4), a vitamin K2 isoform present at high concentrations in the brain, kidney and pancreas. Mediates the conversion of phylloquinone (PK) into menaquinone-4 (MK-4), probably by cleaving the side chain of phylloquinone (PK) to release 2-methyl-1,4-naphthoquinone (menadione; K3) and then prenylating it with geranylgeranyl pyrophosphate (GGPP) to form MK-4.
PATHWAY: Cofactor biosynthesis; menaquinone biosynthesis.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein. Cytoplasm. Nucleus. Mitochondrion.
TISSUE SPECIFICITY: Ubiquitously expressed.
DISEASE: Defects in UBIAD1 are the cause of crystalline corneal dystrophy of Schnyder (SCCD) [MIM:121800]. SCCD is a rare autosomal dominant disease characterized by progressive corneal opacification resulting from abnormal deposition of cholesterol and phospholipids.
MISCELLANEOUS: Strongly down-regulated in transitional cell carcinoma of the bladder and in prostate carcinoma (at protein level).
SIMILARITY: Belongs to the UbiA prenyltransferase family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): UBIAD1
CDC HuGE Published Literature: UBIAD1
Positive Disease Associations: Heart Failure
Related Studies:
  1. Heart Failure
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: UBIAD1
Diseases sorted by gene-association score: corneal dystrophy, schnyder type* (1340), corneal dystrophy (27), transitional cell carcinoma (14), stromal dystrophy (9), macular corneal dystrophy (7), corneal disease (4), renal clear cell carcinoma (2)
* = 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
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.25 RPKM in Testis
Total median expression: 171.61 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 -164.70334-0.493 Picture PostScript Text
3' UTR -804.562303-0.349 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
IPR000537 - UbiA_prenyltransferase
IPR026046 - UBIAD1

Pfam Domains:
PF01040 - UbiA prenyltransferase family

ModBase Predicted Comparative 3D Structure on Q9Y5Z9
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004659 prenyltransferase activity
GO:0005515 protein binding
GO:0016209 antioxidant activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups

Biological Process:
GO:0006744 ubiquinone biosynthetic process
GO:0009234 menaquinone biosynthetic process
GO:0032194 ubiquinone biosynthetic process via 3,4-dihydroxy-5-polyprenylbenzoate
GO:0042371 vitamin K biosynthetic process
GO:0042373 vitamin K metabolic process
GO:0098869 cellular oxidant detoxification

Cellular Component:
GO:0000139 Golgi membrane
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030173 integral component of Golgi membrane
GO:0031966 mitochondrial membrane


-  Descriptions from all associated GenBank mRNAs
  LF206724 - JP 2014500723-A/14227: Polycomb-Associated Non-Coding RNAs.
AK222808 - Homo sapiens mRNA for transitional epithelia response protein variant, clone: HEP04214.
AK074890 - Homo sapiens cDNA FLJ90409 fis, clone NT2RP2006580, highly similar to UbiA prenyltransferase domain-containing protein 1.
AF117064 - Homo sapiens transitional epithelia response protein (TERE1) mRNA, complete cds.
JD542143 - Sequence 523167 from Patent EP1572962.
JD203477 - Sequence 184501 from Patent EP1572962.
JD400152 - Sequence 381176 from Patent EP1572962.
JD400153 - Sequence 381177 from Patent EP1572962.
BC004468 - Homo sapiens UbiA prenyltransferase domain containing 1, mRNA (cDNA clone MGC:10310 IMAGE:3936638), complete cds.
KJ893708 - Synthetic construct Homo sapiens clone ccsbBroadEn_03102 UBIAD1 gene, encodes complete protein.
JD355635 - Sequence 336659 from Patent EP1572962.
BT006832 - Homo sapiens transitional epithelia response protein mRNA, complete cds.
LF357372 - JP 2014500723-A/164875: Polycomb-Associated Non-Coding RNAs.
LF357371 - JP 2014500723-A/164874: Polycomb-Associated Non-Coding RNAs.
AY044167 - Homo sapiens clone IMAGE:BE741130 mRNA sequence.
AK027433 - Homo sapiens cDNA FLJ14527 fis, clone NT2RM2000006.
LF357367 - JP 2014500723-A/164870: Polycomb-Associated Non-Coding RNAs.
AK074487 - Homo sapiens cDNA FLJ90006 fis, clone HEMBA1000121.
JD481349 - Sequence 462373 from Patent EP1572962.
DQ572594 - Homo sapiens piRNA piR-40706, complete sequence.
MA442301 - JP 2018138019-A/14227: Polycomb-Associated Non-Coding RNAs.
MA592949 - JP 2018138019-A/164875: Polycomb-Associated Non-Coding RNAs.
MA592948 - JP 2018138019-A/164874: Polycomb-Associated Non-Coding RNAs.
MA592944 - JP 2018138019-A/164870: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-5870 - ubiquinol-8 biosynthesis (eukaryotic)

Reactome (by CSHL, EBI, and GO)

Protein Q9Y5Z9 (Reactome details) participates in the following event(s):

R-HSA-6806674 UBIA1D prenylates menadione to form MK4 (vitamin K hydroquinone)
R-HSA-6806664 Metabolism of vitamin K
R-HSA-6806667 Metabolism of fat-soluble vitamins
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B3KQG3, NM_013319, NP_037451, Q53GX3, Q5THD4, Q9Y5Z9, TERE1, UBIA1_HUMAN
UCSC ID: uc001asg.3
RefSeq Accession: NM_013319
Protein: Q9Y5Z9 (aka UBIA1_HUMAN)
CCDS: CCDS129.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_013319.2
exon count: 2CDS single in 3' UTR: no RNA size: 3687
ORF size: 1017CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2213.00frame shift in genome: no % Coverage: 99.11
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.