Human Gene RPF2 (ENST00000441448.7_4) from GENCODE V47lift37
  Description: ribosome production factor 2 homolog, transcript variant 1 (from RefSeq NM_032194.3)
Gencode Transcript: ENST00000441448.7_4
Gencode Gene: ENSG00000197498.13_7
Transcript (Including UTRs)
   Position: hg19 chr6:111,303,241-111,349,466 Size: 46,226 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr6:111,303,310-111,346,785 Size: 43,476 Coding Exon Count: 10 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:111,303,241-111,349,466)mRNA (may differ from genome)Protein (306 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RPF2_HUMAN
DESCRIPTION: RecName: Full=Ribosome production factor 2 homolog; AltName: Full=Brix domain-containing protein 1; AltName: Full=Ribosome biogenesis protein RPF2 homolog;
SUBCELLULAR LOCATION: Nucleus, nucleolus. Note=Associated with the nucleolus in an RNA-dependent manner.
SIMILARITY: Belongs to the RPF2 family.
SIMILARITY: Contains 1 Brix domain.

-  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: 12.23 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 272.01 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 -23.1069-0.335 Picture PostScript Text
3' UTR -735.902681-0.274 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
IPR007109 - Brix

Pfam Domains:
PF04427 - Brix domain

SCOP Domains:
52954 - Class II aaRS ABD-related

ModBase Predicted Comparative 3D Structure on Q9H7B2
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
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0008097 5S rRNA binding
GO:0019843 rRNA binding

Biological Process:
GO:0000027 ribosomal large subunit assembly
GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0042254 ribosome biogenesis
GO:0042273 ribosomal large subunit biogenesis
GO:1901796 regulation of signal transduction by p53 class mediator
GO:1902570 protein localization to nucleolus

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  HQ447186 - Synthetic construct Homo sapiens clone IMAGE:100070480; CCSB002625_01 brix domain containing 1 (BXDC1) gene, encodes complete protein.
KJ899759 - Synthetic construct Homo sapiens clone ccsbBroadEn_09153 RPF2 gene, encodes complete protein.
AK292165 - Homo sapiens cDNA FLJ76924 complete cds, highly similar to Homo sapiens brix domain containing 1 (BXDC1), mRNA.
AK024740 - Homo sapiens cDNA: FLJ21087 fis, clone CAS03323.
AK301662 - Homo sapiens cDNA FLJ57639 complete cds, highly similar to Brix domain-containing protein 1.
AL833613 - Homo sapiens mRNA; cDNA DKFZp686A1873 (from clone DKFZp686A1873).
BC005347 - Homo sapiens cDNA clone IMAGE:3934284, containing frame-shift errors.
BC035314 - Homo sapiens brix domain containing 1, mRNA (cDNA clone MGC:21067 IMAGE:4745524), complete cds.
LF384627 - JP 2014500723-A/192130: Polycomb-Associated Non-Coding RNAs.
CU690066 - Synthetic construct Homo sapiens gateway clone IMAGE:100018100 5' read BXDC1 mRNA.
LF322208 - JP 2014500723-A/129711: Polycomb-Associated Non-Coding RNAs.
LF322207 - JP 2014500723-A/129710: Polycomb-Associated Non-Coding RNAs.
JD041940 - Sequence 22964 from Patent EP1572962.
LF322206 - JP 2014500723-A/129709: Polycomb-Associated Non-Coding RNAs.
JD393565 - Sequence 374589 from Patent EP1572962.
JD228935 - Sequence 209959 from Patent EP1572962.
JD182279 - Sequence 163303 from Patent EP1572962.
JD298301 - Sequence 279325 from Patent EP1572962.
JD289956 - Sequence 270980 from Patent EP1572962.
JD525024 - Sequence 506048 from Patent EP1572962.
JD222679 - Sequence 203703 from Patent EP1572962.
JD196711 - Sequence 177735 from Patent EP1572962.
JD189121 - Sequence 170145 from Patent EP1572962.
JD411400 - Sequence 392424 from Patent EP1572962.
AK056264 - Homo sapiens cDNA FLJ31702 fis, clone NT2RI2006081.
JD064529 - Sequence 45553 from Patent EP1572962.
JD550030 - Sequence 531054 from Patent EP1572962.
JD500924 - Sequence 481948 from Patent EP1572962.
JD291164 - Sequence 272188 from Patent EP1572962.
JD527575 - Sequence 508599 from Patent EP1572962.
JD160998 - Sequence 142022 from Patent EP1572962.
JD246426 - Sequence 227450 from Patent EP1572962.
JD146328 - Sequence 127352 from Patent EP1572962.
JD351074 - Sequence 332098 from Patent EP1572962.
JD513024 - Sequence 494048 from Patent EP1572962.
JD098375 - Sequence 79399 from Patent EP1572962.
JD337689 - Sequence 318713 from Patent EP1572962.
JD463228 - Sequence 444252 from Patent EP1572962.
JD151193 - Sequence 132217 from Patent EP1572962.
JD255804 - Sequence 236828 from Patent EP1572962.
JD425917 - Sequence 406941 from Patent EP1572962.
JD070787 - Sequence 51811 from Patent EP1572962.
JD133358 - Sequence 114382 from Patent EP1572962.
JD153774 - Sequence 134798 from Patent EP1572962.
JD142889 - Sequence 123913 from Patent EP1572962.
JD091566 - Sequence 72590 from Patent EP1572962.
JD067395 - Sequence 48419 from Patent EP1572962.
JD317114 - Sequence 298138 from Patent EP1572962.
JD273289 - Sequence 254313 from Patent EP1572962.
JD457389 - Sequence 438413 from Patent EP1572962.
JD311494 - Sequence 292518 from Patent EP1572962.
JD234785 - Sequence 215809 from Patent EP1572962.
JD082016 - Sequence 63040 from Patent EP1572962.
JD336140 - Sequence 317164 from Patent EP1572962.
JD192239 - Sequence 173263 from Patent EP1572962.
JD130858 - Sequence 111882 from Patent EP1572962.
JD425839 - Sequence 406863 from Patent EP1572962.
JD241434 - Sequence 222458 from Patent EP1572962.
JD498951 - Sequence 479975 from Patent EP1572962.
JD556092 - Sequence 537116 from Patent EP1572962.
JD415644 - Sequence 396668 from Patent EP1572962.
JD122202 - Sequence 103226 from Patent EP1572962.
JD384782 - Sequence 365806 from Patent EP1572962.
JD396788 - Sequence 377812 from Patent EP1572962.
JD313746 - Sequence 294770 from Patent EP1572962.
JD154579 - Sequence 135603 from Patent EP1572962.
JD044447 - Sequence 25471 from Patent EP1572962.
JD355028 - Sequence 336052 from Patent EP1572962.
JD248979 - Sequence 230003 from Patent EP1572962.
JD513316 - Sequence 494340 from Patent EP1572962.
JD379444 - Sequence 360468 from Patent EP1572962.
JD429003 - Sequence 410027 from Patent EP1572962.
JD170793 - Sequence 151817 from Patent EP1572962.
JD285066 - Sequence 266090 from Patent EP1572962.
JD237984 - Sequence 219008 from Patent EP1572962.
JD553419 - Sequence 534443 from Patent EP1572962.
MA620204 - JP 2018138019-A/192130: Polycomb-Associated Non-Coding RNAs.
MA557785 - JP 2018138019-A/129711: Polycomb-Associated Non-Coding RNAs.
MA557784 - JP 2018138019-A/129710: Polycomb-Associated Non-Coding RNAs.
MA557783 - JP 2018138019-A/129709: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: BXDC1, ENST00000441448.1, ENST00000441448.2, ENST00000441448.3, ENST00000441448.4, ENST00000441448.5, ENST00000441448.6, NM_032194, Q5VXN1, Q8N4A1, Q9H7B2, RPF2_HUMAN, uc320jot.1, uc320jot.2
UCSC ID: ENST00000441448.7_4
RefSeq Accession: NM_032194.3
Protein: Q9H7B2 (aka RPF2_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.