Human Gene NAF1 (uc003iqj.3) Description and Page Index
  Description: Homo sapiens nuclear assembly factor 1 ribonucleoprotein (NAF1), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr4:164,049,823-164,088,073 Size: 38,251 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 CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:164,049,823-164,088,073)mRNA (may differ from genome)Protein (494 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
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H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  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.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NAF1
CDC HuGE Published Literature: NAF1

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

+  Common Gene Haplotype Alleles
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-  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
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -74.90194-0.386 Picture PostScript Text
3' UTR -39.20226-0.173 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

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

2EQN
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q96HR8
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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
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
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 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  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, NAF1_HUMAN, NM_138386, NP_612395, Q96HR8
UCSC ID: uc003iqj.3
RefSeq Accession: NM_138386
Protein: Q96HR8 (aka NAF1_HUMAN)
CCDS: CCDS3803.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_138386.2
exon count: 8CDS single in 3' UTR: no RNA size: 1918
ORF size: 1485CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3122.00frame shift in genome: no % Coverage: 99.32
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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.