Human Gene UTP3 (ENST00000254803.4_4) from GENCODE V47lift37
  Description: UTP3 small subunit processome component (from RefSeq NM_020368.3)
Gencode Transcript: ENST00000254803.4_4
Gencode Gene: ENSG00000132467.4_7
Transcript (Including UTRs)
   Position: hg19 chr4:71,554,249-71,556,268 Size: 2,020 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr4:71,554,395-71,555,834 Size: 1,440 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:71,554,249-71,556,268)mRNA (may differ from genome)Protein (479 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SAS10_HUMAN
DESCRIPTION: RecName: Full=Something about silencing protein 10; AltName: Full=Charged amino acid-rich leucine zipper 1; Short=CRL1; AltName: Full=Disrupter of silencing SAS10; AltName: Full=UTP3 homolog;
FUNCTION: Essential for gene silencing: has a role in the structure of silenced chromatin. Plays a role in the developing brain (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the SAS10 family.

-  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: UTP3
Diseases sorted by gene-association score: common bile duct disease (2)

-  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: 29.51 RPKM in Spleen
Total median expression: 555.97 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 -43.40146-0.297 Picture PostScript Text
3' UTR -94.60434-0.218 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
IPR007146 - Sas10/Utp3/C1D
IPR018972 - Sas10_C_dom

Pfam Domains:
PF04000 - Sas10/Utp3/C1D family
PF09368 - Sas10 C-terminal domain

ModBase Predicted Comparative 3D Structure on Q9NQZ2
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 orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006325 chromatin organization
GO:0006364 rRNA processing
GO:0007275 multicellular organism development
GO:0007420 brain development

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0032040 small-subunit processome


-  Descriptions from all associated GenBank mRNAs
  AF271212 - Homo sapiens disrupter of silencing SAS10 (SAS10) mRNA, complete cds.
AK026909 - Homo sapiens cDNA: FLJ23256 fis, clone COL05534.
BC004546 - Homo sapiens UTP3, small subunit (SSU) processome component, homolog (S. cerevisiae), mRNA (cDNA clone MGC:11290 IMAGE:3946633), complete cds.
AL136590 - Homo sapiens mRNA; cDNA DKFZp761F222 (from clone DKFZp761F222).
AB463337 - Synthetic construct DNA, clone: pF1KB8692, Homo sapiens UTP3 gene for UTP3, small subunit (SSU) processome component, homolog, without stop codon, in Flexi system.
AM392862 - Synthetic construct Homo sapiens clone IMAGE:100001994 for hypothetical protein (SAS10 gene).
AM393072 - Synthetic construct Homo sapiens clone IMAGE:100001988 for hypothetical protein (SAS10 gene).
AM393229 - Synthetic construct Homo sapiens clone IMAGE:100001722 for hypothetical protein (SAS10 gene).
DQ892999 - Synthetic construct clone IMAGE:100005629; FLH191526.01X; RZPDo839E0377D disrupter of silencing 10 (SAS10) gene, encodes complete protein.
EU176750 - Synthetic construct Homo sapiens clone IMAGE:100011529; FLH191525.01L; RZPDo839B12255D disrupter of silencing 10 (SAS10) gene, encodes complete protein.
CU678762 - Synthetic construct Homo sapiens gateway clone IMAGE:100020291 5' read UTP3 mRNA.
KJ894380 - Synthetic construct Homo sapiens clone ccsbBroadEn_03774 UTP3 gene, encodes complete protein.
CR533544 - Homo sapiens full open reading frame cDNA clone RZPDo834F0819D for gene SAS10, disrupter of silencing 10; complete cds, incl. stopcodon.
JD296159 - Sequence 277183 from Patent EP1572962.
JD092600 - Sequence 73624 from Patent EP1572962.
JD549390 - Sequence 530414 from Patent EP1572962.
MP014830 - Sequence 33 from Patent WO2019016252.

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

Protein Q9NQZ2 (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: CRLZ1, ENST00000254803.1, ENST00000254803.2, ENST00000254803.3, NM_020368, Q6FI82, Q9NQZ2, SAS10 , SAS10_HUMAN, uc317fpp.1, uc317fpp.2, UTP3
UCSC ID: ENST00000254803.4_4
RefSeq Accession: NM_020368.3
Protein: Q9NQZ2 (aka SAS10_HUMAN)

-  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.