Human Gene UTP6 (uc002hgr.3) Description and Page Index
  Description: Homo sapiens UTP6, small subunit (SSU) processome component, homolog (yeast) (UTP6), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr17:30,190,190-30,228,729 Size: 38,540 Total Exon Count: 19 Strand: -
Coding Region
   Position: hg19 chr17:30,190,378-30,228,646 Size: 38,269 Coding Exon Count: 19 

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 (chr17:30,190,190-30,228,729)mRNA (may differ from genome)Protein (597 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: UTP6_HUMAN
DESCRIPTION: RecName: Full=U3 small nucleolar RNA-associated protein 6 homolog; AltName: Full=Hepatocellular carcinoma-associated antigen 66; AltName: Full=Multiple hat domains protein;
FUNCTION: Involved in nucleolar processing of pre-18S ribosomal RNA (By similarity).
SUBCELLULAR LOCATION: Nucleus, nucleolus.
SIMILARITY: Belongs to the UTP6 family.
SIMILARITY: Contains 5 HAT repeats.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): UTP6
CDC HuGE Published Literature: UTP6
Positive Disease Associations: Fibrinogen
Related Studies:
  1. Fibrinogen
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: UTP6
Diseases sorted by gene-association score: chromosome 17q11.2 deletion syndrome, 1.4-mb (13), deep keratitis (11), interstitial keratitis (8), congenital syphilis (7)

-  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: 14.94 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 390.26 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 -31.6083-0.381 Picture PostScript Text
3' UTR -38.80188-0.206 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
IPR003107 - HAT
IPR011990 - TPR-like_helical
IPR013949 - U3_snoRNA_assoc-6

Pfam Domains:
PF08640 - U3 small nucleolar RNA-associated protein 6

SCOP Domains:
48439 - Protein prenylyltransferase
48452 - TPR-like

ModBase Predicted Comparative 3D Structure on Q9NYH9
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:0030515 snoRNA binding

Biological Process:
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006364 rRNA processing
GO:0006396 RNA processing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0032040 small-subunit processome
GO:0034388 Pwp2p-containing subcomplex of 90S preribosome


-  Descriptions from all associated GenBank mRNAs
  AJ272197 - Homo sapiens partial mRNA for hypothetical protein, 830bp.
BC015454 - Homo sapiens UTP6, small subunit (SSU) processome component, homolog (yeast), mRNA (cDNA clone IMAGE:4430701), partial cds.
BC035325 - Homo sapiens UTP6, small subunit (SSU) processome component, homolog (yeast), mRNA (cDNA clone MGC:34283 IMAGE:5188856), complete cds.
AF334386 - Homo sapiens multiple hat domains (MHAT) mRNA, complete cds.
LF384774 - JP 2014500723-A/192277: Polycomb-Associated Non-Coding RNAs.
AF116631 - Homo sapiens PRO1289 mRNA, complete cds.
AF244135 - Homo sapiens hepatocellular carcinoma-associated antigen 66 (HCA66) mRNA, complete cds.
AK126564 - Homo sapiens cDNA FLJ44601 fis, clone BLADE2007799, highly similar to U3 small nucleolar RNA-associated protein 6 homolog.
AK057202 - Homo sapiens cDNA FLJ32640 fis, clone SYNOV2001033, highly similar to U3 small nucleolar RNA-associated protein 6 homolog.
JD375683 - Sequence 356707 from Patent EP1572962.
JD358918 - Sequence 339942 from Patent EP1572962.
AK225448 - Homo sapiens mRNA for Hepatocellular carcinoma-associated antigen 66 variant, clone: HSI05173.
KJ899198 - Synthetic construct Homo sapiens clone ccsbBroadEn_08592 UTP6 gene, encodes complete protein.
AB527664 - Synthetic construct DNA, clone: pF1KB6153, Homo sapiens UTP6 gene for UTP6, small subunit (SSU) processome component, homolog, without stop codon, in Flexi system.
LF326933 - JP 2014500723-A/134436: Polycomb-Associated Non-Coding RNAs.
AK315929 - Homo sapiens cDNA, FLJ78828 complete cds, highly similar to U3 small nucleolar RNA-associated protein 6 homolog.
AK299806 - Homo sapiens cDNA FLJ58748 complete cds, highly similar to U3 small nucleolar RNA-associated protein 6homolog.
LF326935 - JP 2014500723-A/134438: Polycomb-Associated Non-Coding RNAs.
LF326936 - JP 2014500723-A/134439: Polycomb-Associated Non-Coding RNAs.
LF326937 - JP 2014500723-A/134440: Polycomb-Associated Non-Coding RNAs.
LF326938 - JP 2014500723-A/134441: Polycomb-Associated Non-Coding RNAs.
LF326939 - JP 2014500723-A/134442: Polycomb-Associated Non-Coding RNAs.
LF326941 - JP 2014500723-A/134444: Polycomb-Associated Non-Coding RNAs.
LF326944 - JP 2014500723-A/134447: Polycomb-Associated Non-Coding RNAs.
LF326946 - JP 2014500723-A/134449: Polycomb-Associated Non-Coding RNAs.
MA620351 - JP 2018138019-A/192277: Polycomb-Associated Non-Coding RNAs.
MA562510 - JP 2018138019-A/134436: Polycomb-Associated Non-Coding RNAs.
MA562512 - JP 2018138019-A/134438: Polycomb-Associated Non-Coding RNAs.
MA562513 - JP 2018138019-A/134439: Polycomb-Associated Non-Coding RNAs.
MA562514 - JP 2018138019-A/134440: Polycomb-Associated Non-Coding RNAs.
MA562515 - JP 2018138019-A/134441: Polycomb-Associated Non-Coding RNAs.
MA562516 - JP 2018138019-A/134442: Polycomb-Associated Non-Coding RNAs.
MA562518 - JP 2018138019-A/134444: Polycomb-Associated Non-Coding RNAs.
MA562521 - JP 2018138019-A/134447: Polycomb-Associated Non-Coding RNAs.
MA562523 - JP 2018138019-A/134449: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9NYH9 (Reactome details) participates in the following event(s):

R-HSA-6790906 EMG1 of the SSU processome methylates pseudouridine-1248 of 18S rRNA yielding N(1)-methylpseudouridine-1248
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-6790901 rRNA modification in the nucleus and cytosol
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: C17orf40, HCA66, MHAT, NM_018428, NP_060898, Q8IX96, Q96BL2, Q9NQ91, Q9NYH9, UTP6_HUMAN
UCSC ID: uc002hgr.3
RefSeq Accession: NM_018428
Protein: Q9NYH9 (aka UTP6_HUMAN)
CCDS: CCDS11269.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018428.2
exon count: 19CDS single in 3' UTR: no RNA size: 2065
ORF size: 1794CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3788.00frame 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.