Human Gene RPF1 (uc001djv.4) Description and Page Index
  Description: Homo sapiens ribosome production factor 1 homolog (S. cerevisiae) (RPF1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:84,944,920-84,964,033 Size: 19,114 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr1:84,944,965-84,963,153 Size: 18,189 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:84,944,920-84,964,033)mRNA (may differ from genome)Protein (349 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RPF1_HUMAN
DESCRIPTION: RecName: Full=Ribosome production factor 1; AltName: Full=Brix domain-containing protein 5; AltName: Full=Ribosome biogenesis protein RPF1;
FUNCTION: May be required for ribosome biogenesis.
SUBCELLULAR LOCATION: Nucleus, nucleolus.
SIMILARITY: Contains 1 Brix domain.
SEQUENCE CAUTION: Sequence=CAH71915.1; Type=Erroneous gene model prediction;

-  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: 21.94 RPKM in Testis
Total median expression: 683.06 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 -14.1045-0.313 Picture PostScript Text
3' UTR -214.66880-0.244 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
IPR004154 - Anticodon-bd
IPR007109 - Brix

Pfam Domains:
PF04427 - Brix domain

ModBase Predicted Comparative 3D Structure on Q9H9Y2
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 BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0019843 rRNA binding
GO:0042134 rRNA primary transcript binding

Biological Process:
GO:0000027 ribosomal large subunit assembly
GO:0000460 maturation of 5.8S rRNA
GO:0000470 maturation of LSU-rRNA
GO:0006364 rRNA processing
GO:0042254 ribosome biogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0030687 preribosome, large subunit precursor


-  Descriptions from all associated GenBank mRNAs
  KJ899612 - Synthetic construct Homo sapiens clone ccsbBroadEn_09006 RPF1 gene, encodes complete protein.
LF206365 - JP 2014500723-A/13868: Polycomb-Associated Non-Coding RNAs.
AK022537 - Homo sapiens cDNA FLJ12475 fis, clone NT2RM1000962.
BC016051 - Homo sapiens brix domain containing 5, mRNA (cDNA clone MGC:22954 IMAGE:4853072), complete cds.
CU677559 - Synthetic construct Homo sapiens gateway clone IMAGE:100018165 5' read BXDC5 mRNA.
HQ447238 - Synthetic construct Homo sapiens clone IMAGE:100070543; CCSB007613_01 brix domain containing 5 (BXDC5) gene, encodes complete protein.
AF322053 - Homo sapiens RNA processing factor 1 (RPF1) mRNA, complete cds.
LF353554 - JP 2014500723-A/161057: Polycomb-Associated Non-Coding RNAs.
AL359584 - Homo sapiens mRNA; cDNA DKFZp761G0415 (from clone DKFZp761G0415).
CR627468 - Homo sapiens mRNA; cDNA DKFZp761M0215 (from clone DKFZp761M0215).
LF353551 - JP 2014500723-A/161054: Polycomb-Associated Non-Coding RNAs.
LF353547 - JP 2014500723-A/161050: Polycomb-Associated Non-Coding RNAs.
LF353546 - JP 2014500723-A/161049: Polycomb-Associated Non-Coding RNAs.
MA441942 - JP 2018138019-A/13868: Polycomb-Associated Non-Coding RNAs.
MA589131 - JP 2018138019-A/161057: Polycomb-Associated Non-Coding RNAs.
MA589128 - JP 2018138019-A/161054: Polycomb-Associated Non-Coding RNAs.
MA589124 - JP 2018138019-A/161050: Polycomb-Associated Non-Coding RNAs.
MA589123 - JP 2018138019-A/161049: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: BXDC5, NM_025065, NP_079341, Q5VSK7, Q6AHX1, Q8WXZ8, Q9H9Y2, RPF1_HUMAN
UCSC ID: uc001djv.4
RefSeq Accession: NM_025065
Protein: Q9H9Y2 (aka RPF1_HUMAN)
CCDS: CCDS695.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_025065.6
exon count: 9CDS single in 3' UTR: no RNA size: 1975
ORF size: 1050CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2299.00frame 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.