Human Gene EBNA1BP2 (ENST00000236051.3_9) from GENCODE V47lift37
  Description: EBNA1 binding protein 2, transcript variant 2 (from RefSeq NM_006824.3)
Gencode Transcript: ENST00000236051.3_9
Gencode Gene: ENSG00000117395.13_12
Transcript (Including UTRs)
   Position: hg19 chr1:43,629,855-43,637,961 Size: 8,107 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr1:43,630,114-43,637,789 Size: 7,676 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:43,629,855-43,637,961)mRNA (may differ from genome)Protein (306 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: EBP2_HUMAN
DESCRIPTION: RecName: Full=Probable rRNA-processing protein EBP2; AltName: Full=EBNA1-binding protein 2; AltName: Full=Nucleolar protein p40;
FUNCTION: Required for the processing of the 27S pre-rRNA (By similarity).
SUBUNIT: Specifically interacts with EBV EBNA1. The EBNA1-EBP2 interaction is important for the stable segregation of EBV episomes during cell division.
SUBCELLULAR LOCATION: Nucleus, nucleolus. Note=Associated with the nucleolus in an RNA-dependent manner.
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the EBP2 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


-  MalaCards Disease Associations
  MalaCards Gene Search: EBNA1BP2
Diseases sorted by gene-association score: early-onset familial alzheimer disease (2)

-  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: 26.58 RPKM in Pituitary
Total median expression: 674.62 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 -73.70172-0.428 Picture PostScript Text
3' UTR -41.10259-0.159 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
IPR008610 - Ebp2

Pfam Domains:
PF05890 - Eukaryotic rRNA processing protein EBP2

ModBase Predicted Comparative 3D Structure on Q99848
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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 orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details   Gene Details
Gene SorterGene Sorter   Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

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

Biological Process:
GO:0006364 rRNA processing
GO:0042254 ribosome biogenesis
GO:0042273 ribosomal large subunit biogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0030687 preribosome, large subunit precursor
GO:0034399 nuclear periphery


-  Descriptions from all associated GenBank mRNAs
  BC073924 - Homo sapiens EBNA1 binding protein 2, mRNA (cDNA clone IMAGE:5188532).
U86602 - Human nucleolar protein p40 mRNA, complete cds.
BC009175 - Homo sapiens EBNA1 binding protein 2, mRNA (cDNA clone MGC:1261 IMAGE:2966681), complete cds.
AK299476 - Homo sapiens cDNA FLJ51285 complete cds, highly similar to Probable rRNA-processing protein EBP2.
AK223455 - Homo sapiens mRNA for EBNA1 binding protein 2 variant, clone: FCC114H07.
AB451256 - Homo sapiens EBNA1BP2 mRNA for EBNA1 binding protein 2, complete cds, clone: FLJ08069AAAN.
CR456975 - Homo sapiens full open reading frame cDNA clone RZPDo834C055D for gene EBNA1BP2, EBNA1 binding protein 2; complete cds, incl. stopcodon.
BT006920 - Homo sapiens EBNA1 binding protein 2 mRNA, complete cds.
KJ893184 - Synthetic construct Homo sapiens clone ccsbBroadEn_02578 EBNA1BP2 gene, encodes complete protein.
AB451381 - Homo sapiens EBNA1BP2 mRNA for EBNA1 binding protein 2, partial cds, clone: FLJ08069AAAF.
AB590504 - Synthetic construct DNA, clone: pFN21AE1844, Homo sapiens EBNA1BP2 gene for EBNA1 binding protein 2, without stop codon, in Flexi system.
AK307440 - Homo sapiens cDNA, FLJ97388.
CU679257 - Synthetic construct Homo sapiens gateway clone IMAGE:100018807 5' read EBNA1BP2 mRNA.
AK295006 - Homo sapiens cDNA FLJ60526 complete cds, highly similar to Probable rRNA-processing protein EBP2.
DL491333 - Novel nucleic acids.
JD261382 - Sequence 242406 from Patent EP1572962.
JD452436 - Sequence 433460 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: EBP2, EBP2_HUMAN, ENST00000236051.1, ENST00000236051.2, NM_006824, Q96A66, Q99848, uc317eau.1, uc317eau.2
UCSC ID: ENST00000236051.3_9
RefSeq Accession: NM_006824.3
Protein: Q99848 (aka EBP2_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.