Human Gene UMOD (uc002dhb.3)
  Description: Homo sapiens uromodulin (UMOD), transcript variant 1, mRNA.
RefSeq Summary (NM_003361): The protein encoded by this gene is the most abundant protein in mammalian urine under physiological conditions. Its excretion in urine follows proteolytic cleavage of the ectodomain of its glycosyl phosphatidylinosital-anchored counterpart that is situated on the luminal cell surface of the loop of Henle. This protein may act as a constitutive inhibitor of calcium crystallization in renal fluids. Excretion of this protein in urine may provide defense against urinary tract infections caused by uropathogenic bacteria. Defects in this gene are associated with the renal disorders medullary cystic kidney disease-2 (MCKD2), glomerulocystic kidney disease with hyperuricemia and isosthenuria (GCKDHI), and familial juvenile hyperuricemic nephropathy (FJHN). Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2013].
Transcript (Including UTRs)
   Position: hg19 chr16:20,344,373-20,364,037 Size: 19,665 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr16:20,344,636-20,362,059 Size: 17,424 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:20,344,373-20,364,037)mRNA (may differ from genome)Protein (673 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: E9PEA4_HUMAN
DESCRIPTION: SubName: Full=Uromodulin;
SIMILARITY: Contains 1 ZP domain.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): UMOD
CDC HuGE Published Literature: UMOD
Positive Disease Associations: Creatinine , Hypertension , Kidney Diseases , Kidney Failure, Chronic , Osteoporosis , renal function and chronic kidney disease , Waist Circumference
Related Studies:
  1. Creatinine
    Anna Kottgen et al. Nature genetics 2009, Multiple loci associated with indices of renal function and chronic kidney disease., Nature genetics. [PubMed 19430482]
  2. Hypertension
    Sandosh Padmanabhan et al. PLoS genetics 2010, Genome-wide association study of blood pressure extremes identifies variant near UMOD associated with hypertension., PLoS genetics. [PubMed 21082022]
  3. Kidney Diseases
    Anna Kottgen et al. Nature genetics 2010, New loci associated with kidney function and chronic kidney disease., Nature genetics. [PubMed 20383146]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: UMOD
Diseases sorted by gene-association score: hyperuricemic nephropathy, familial juvenile 1* (1681), medullary cystic kidney disease 2* (1252), glomerulocystic kidney disease with hyperuricemia and isosthenuria* (1242), autosomal dominant medullary cystic kidney disease with hyperuricemia* (750), autosomal dominant tubulointerstitial kidney disease, umod-related* (500), familial juvenile hyperuricaemic nephropathy* (419), hyperuricemia (67), cystic kidney disease (42), kidney disease (37), gout (37), end stage renal failure (35), urinary system disease (16), cystitis (16), interstitial nephritis (13), nephrolithiasis, calcium oxalate (10), chronic pyelonephritis (10), vesicoureteral reflux (10), acute kidney tubular necrosis (9), nephrolithiasis (8), fabry disease (7), urinary tract obstruction (7), interstitial cystitis (7), xanthinuria, type i (7), nephronophthisis (7), pyelonephritis (6), bartter disease (5), congenital disorder of glycosylation, type in (5), chronic kidney failure (3)
* = 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: 271.11 RPKM in Kidney - Cortex
Total median expression: 273.14 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 -35.80129-0.278 Picture PostScript Text
3' UTR -80.70263-0.307 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
IPR000742 - EG-like_dom
IPR001881 - EGF-like_Ca-bd
IPR013032 - EGF-like_CS
IPR000152 - EGF-type_Asp/Asn_hydroxyl_site
IPR018097 - EGF_Ca-bd_CS
IPR024731 - EGF_dom_MSP1-like
IPR009030 - Growth_fac_rcpt
IPR001507 - ZP_dom
IPR017977 - ZP_dom_CS

Pfam Domains:
PF00008 - EGF-like domain
PF00100 - Zona pellucida-like domain
PF07645 - Calcium-binding EGF domain
PF12661 - Human growth factor-like EGF
PF12947 - EGF domain

SCOP Domains:
57196 - EGF/Laminin
57184 - Growth factor receptor domain

ModBase Predicted Comparative 3D Structure on E9PEA4
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  M17778 - Human uromodulin (Tamm-Horsfall glycoprotein) mRNA, complete cds.
AK127643 - Homo sapiens cDNA FLJ45741 fis, clone KIDNE2015987, highly similar to Uromodulin precursor.
AK055722 - Homo sapiens cDNA FLJ31160 fis, clone KIDNE1000015, highly similar to UROMODULIN PRECURSOR.
AK091961 - Homo sapiens cDNA FLJ34642 fis, clone KIDNE2016918, highly similar to UROMODULIN PRECURSOR.
AK096043 - Homo sapiens cDNA FLJ38724 fis, clone KIDNE2010151, highly similar to UROMODULIN PRECURSOR.
AX747279 - Sequence 804 from Patent EP1308459.
M15881 - Human uromodulin (Tamm-Horsfall glycoprotein) mRNA, complete cds.
AK127648 - Homo sapiens cDNA FLJ45746 fis, clone KIDNE2018727, highly similar to Uromodulin precursor.
BC035975 - Homo sapiens uromodulin, mRNA (cDNA clone MGC:32619 IMAGE:4556427), complete cds.
JD075690 - Sequence 56714 from Patent EP1572962.
JD402899 - Sequence 383923 from Patent EP1572962.
JD537622 - Sequence 518646 from Patent EP1572962.
JD231069 - Sequence 212093 from Patent EP1572962.
JD277850 - Sequence 258874 from Patent EP1572962.
JD251636 - Sequence 232660 from Patent EP1572962.
AB590834 - Synthetic construct DNA, clone: pFN21AE2038, Homo sapiens UMOD gene for uromodulin, without stop codon, in Flexi system.
JD020697 - Sequence 1721 from Patent EP1572962.
JD033330 - Sequence 14354 from Patent EP1572962.
CU690246 - Synthetic construct Homo sapiens gateway clone IMAGE:100022010 5' read UMOD mRNA.
JD079103 - Sequence 60127 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AX747279, E9PEA4, E9PEA4_HUMAN, NM_003361, NP_003352
UCSC ID: uc002dhb.3
RefSeq Accession: NM_003361
Protein: E9PEA4 CCDS: CCDS10583.1, CCDS61876.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene UMOD:
mckd2 (Autosomal Dominant Tubulointerstitial Kidney Disease -- UMOD)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AX747279.1
exon count: 12CDS single in 3' UTR: no RNA size: 2408
ORF size: 2022CDS single in intron: no Alignment % ID: 99.83
txCdsPredict score: 4244.00frame shift in genome: no % Coverage: 100.00
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.