Human Gene UTP14A (ENST00000425117.6) from GENCODE V44
  Description: Homo sapiens UTP14A small subunit processome component (UTP14A), transcript variant 2, mRNA. (from RefSeq NM_001166221)
RefSeq Summary (NM_001166221): This gene encodes a member of the uridine triphosphate 14 family. As an essential component of a large ribonucleoprotein complex bound to the U3 small nucleolar RNA, the encoded protein is involved in ribosome biogenesis and 18S rRNA synthesis. An autosomal retrotransposed copy of this X-linked gene exists on chromosome 13. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009].
Gencode Transcript: ENST00000425117.6
Gencode Gene: ENSG00000156697.13
Transcript (Including UTRs)
   Position: hg38 chrX:129,906,121-129,929,761 Size: 23,641 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg38 chrX:129,906,211-129,929,608 Size: 23,398 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:129,906,121-129,929,761)mRNA (may differ from genome)Protein (719 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: UT14A_HUMAN
DESCRIPTION: RecName: Full=U3 small nucleolar RNA-associated protein 14 homolog A; AltName: Full=Antigen NY-CO-16; AltName: Full=Serologically defined colon cancer antigen 16;
FUNCTION: May be required for ribosome biogenesis (By similarity).
INTERACTION: O95257:GADD45G; NbExp=2; IntAct=EBI-473284, EBI-448202;
SUBCELLULAR LOCATION: Nucleus, nucleolus.
TISSUE SPECIFICITY: Ubiquitously expressed.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
MISCELLANEOUS: The human genome also contains the UTP14C gene, an autosomal retrotransposed copy of this X-linked gene. Evolution of autosomal retrogenes from X-linked progenitors compensates for X- chromosome silencing during male meiosis.
SIMILARITY: Belongs to the UTP14 family.
SEQUENCE CAUTION: Sequence=CAI42909.1; Type=Erroneous gene model prediction;

-  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


-  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: 9.01 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 201.31 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 -21.1090-0.234 Picture PostScript Text
3' UTR -40.10153-0.262 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
IPR006709 - SSU_processome_Utp14

Pfam Domains:
PF04615 - Utp14 protein

ModBase Predicted Comparative 3D Structure on Q9BVJ6
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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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

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

Biological Process:
GO:0006364 rRNA processing
GO:0030490 maturation of SSU-rRNA
GO:0042254 ribosome biogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005829 cytosol
GO:0032040 small-subunit processome


-  Descriptions from all associated GenBank mRNAs
  LP896571 - Sequence 1435 from Patent EP3253886.
AK291918 - Homo sapiens cDNA FLJ76903 complete cds, highly similar to Homo sapiens UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast) (UTP14A), mRNA.
AK298578 - Homo sapiens cDNA FLJ53406 complete cds, highly similar to U3 small nucleolar RNA-associated protein 14 homolog A.
BC009649 - Homo sapiens UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast), mRNA (cDNA clone MGC:5577 IMAGE:3459192), complete cds.
BC001149 - Homo sapiens UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast), mRNA (cDNA clone MGC:1291 IMAGE:3355662), complete cds.
AK304563 - Homo sapiens cDNA FLJ54249 complete cds, highly similar to U3 small nucleolar RNA-associated protein 14 homolog A.
BC014987 - Homo sapiens UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast), mRNA (cDNA clone MGC:23217 IMAGE:4901477), complete cds.
AF039694 - Homo sapiens antigen NY-CO-16 mRNA, complete cds.
CU679427 - Synthetic construct Homo sapiens gateway clone IMAGE:100020072 5' read UTP14A mRNA.
AB590128 - Synthetic construct DNA, clone: pFN21AE1533, Homo sapiens UTP14A gene for UTP14, U3 small nucleolar ribonucleoprotein, homolog A, without stop codon, in Flexi system.
DQ892549 - Synthetic construct clone IMAGE:100005179; FLH187385.01X; RZPDo839G0972D UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast) (UTP14A) gene, encodes complete protein.
DQ895760 - Synthetic construct Homo sapiens clone IMAGE:100010220; FLH187381.01L; RZPDo839G0962D UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast) (UTP14A) gene, encodes complete protein.
KJ893140 - Synthetic construct Homo sapiens clone ccsbBroadEn_02534 UTP14A gene, encodes complete protein.
AK094408 - Homo sapiens cDNA FLJ37089 fis, clone BRACE2017298, weakly similar to Translation initiation factor eIF3.
LF211469 - JP 2014500723-A/18972: Polycomb-Associated Non-Coding RNAs.
MA447046 - JP 2018138019-A/18972: Polycomb-Associated Non-Coding RNAs.
LF380016 - JP 2014500723-A/187519: Polycomb-Associated Non-Coding RNAs.
MA615593 - JP 2018138019-A/187519: Polycomb-Associated Non-Coding RNAs.
LF380017 - JP 2014500723-A/187520: Polycomb-Associated Non-Coding RNAs.
MA615594 - JP 2018138019-A/187520: Polycomb-Associated Non-Coding RNAs.
LF380018 - JP 2014500723-A/187521: Polycomb-Associated Non-Coding RNAs.
MA615595 - JP 2018138019-A/187521: Polycomb-Associated Non-Coding RNAs.
LF380019 - JP 2014500723-A/187522: Polycomb-Associated Non-Coding RNAs.
MA615596 - JP 2018138019-A/187522: Polycomb-Associated Non-Coding RNAs.
LF380020 - JP 2014500723-A/187523: Polycomb-Associated Non-Coding RNAs.
MA615597 - JP 2018138019-A/187523: Polycomb-Associated Non-Coding RNAs.
LF380021 - JP 2014500723-A/187524: Polycomb-Associated Non-Coding RNAs.
MA615598 - JP 2018138019-A/187524: Polycomb-Associated Non-Coding RNAs.
JD455241 - Sequence 436265 from Patent EP1572962.
JD374814 - Sequence 355838 from Patent EP1572962.

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

Protein Q9BVJ6 (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: A8K7A3, A8MVQ1, ENST00000425117.1, ENST00000425117.2, ENST00000425117.3, ENST00000425117.4, ENST00000425117.5, NM_001166221, Q5JYF1, Q9BVJ6, SDCCAG16, uc011mup.1, uc011mup.2, uc011mup.3, UT14A_HUMAN
UCSC ID: ENST00000425117.6
RefSeq Accession: NM_001166221
Protein: Q9BVJ6 (aka UT14A_HUMAN)
CCDS: CCDS55489.1

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