Human Gene NAF1 (ENST00000274054.3_11) from GENCODE V47lift37
  Description: nuclear assembly factor 1 ribonucleoprotein, transcript variant 1 (from RefSeq NM_138386.3)
Gencode Transcript: ENST00000274054.3_11
Gencode Gene: ENSG00000145414.9_13
Transcript (Including UTRs)
   Position: hg19 chr4:164,049,821-164,088,042 Size: 38,222 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr4:164,050,049-164,087,879 Size: 37,831 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:164,049,821-164,088,042)mRNA (may differ from genome)Protein (494 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NAF1_HUMAN
DESCRIPTION: RecName: Full=H/ACA ribonucleoprotein complex non-core subunit NAF1; Short=hNAF1;
FUNCTION: RNA-binding protein required for the maturation of box H/ACA snoRNPs complex and ribosome biogenesis. During assembly of the H/ACA snoRNPs complex, it associates with the complex and disappears during maturation of the complex and is replaced by NOLA1/GAR1 to yield mature H/ACA snoRNPs complex. Probably competes with NOLA1/GAR1 for binding with DKC1/NOLA4.
SUBUNIT: During assembly of the complex, component of the small nucleolar ribonucleoprotein particles containing H/ACA-type snoRNAs (H/ACA snoRNPs) which contains NOLA2/NHP2, NOLA3/NOP10, NAF1 and DKC1/NOLA4. Interacts directly with DKC1/NOLA4.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Shuttles between the cytoplasm and the nucleus. Absent from the nucleolus (By similarity).
SIMILARITY: Belongs to the NAF1 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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 6.95 RPKM in Testis
Total median expression: 164.56 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 -57.70163-0.354 Picture PostScript Text
3' UTR -35.80228-0.157 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
IPR007504 - H/ACA_rnp_Gar1/Naf1
IPR009000 - Transl_elong_init/rib_B-barrel

Pfam Domains:
PF04410 - Gar1/Naf1 RNA binding region

SCOP Domains:
50447 - Translation proteins

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2EQN - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q96HR8
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 orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGD  WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0070034 telomerase RNA binding

Biological Process:
GO:0000454 snoRNA guided rRNA pseudouridine synthesis
GO:0000493 box H/ACA snoRNP assembly
GO:0001522 pseudouridine synthesis
GO:0006364 rRNA processing
GO:0032212 positive regulation of telomere maintenance via telomerase
GO:0042254 ribosome biogenesis
GO:0043489 RNA stabilization
GO:0051973 positive regulation of telomerase activity
GO:0090669 telomerase RNA stabilization
GO:1904358 positive regulation of telomere maintenance via telomere lengthening
GO:1904874 positive regulation of telomerase RNA localization to Cajal body
GO:1905323 telomerase holoenzyme complex assembly

Cellular Component:
GO:0005634 nucleus
GO:0005732 small nucleolar ribonucleoprotein complex
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK308601 - Homo sapiens cDNA, FLJ98642.
BC008207 - Homo sapiens nuclear assembly factor 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:5406 IMAGE:3447276), complete cds.
JD511258 - Sequence 492282 from Patent EP1572962.
JD353935 - Sequence 334959 from Patent EP1572962.
KJ899943 - Synthetic construct Homo sapiens clone ccsbBroadEn_09337 NAF1 gene, encodes complete protein.
AK097352 - Homo sapiens cDNA FLJ40033 fis, clone STOMA2009289.
JD312826 - Sequence 293850 from Patent EP1572962.
JD214730 - Sequence 195754 from Patent EP1572962.
JD232240 - Sequence 213264 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: D3DP28, E9PAZ2, ENST00000274054.1, ENST00000274054.2, NAF1_HUMAN, NM_138386, Q96HR8, uc317jdt.1, uc317jdt.2
UCSC ID: ENST00000274054.3_11
RefSeq Accession: NM_138386.3
Protein: Q96HR8 (aka NAF1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene NAF1:
dkc (Dyskeratosis Congenita and Related Telomere Biology Disorders)
pf (Pulmonary Fibrosis Predisposition Overview)

-  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.