Human Gene YBEY (ENST00000397701.9_4) from GENCODE V47lift37
  Description: ybeY metalloendoribonuclease, transcript variant 6 (from RefSeq NM_001314025.2)
Gencode Transcript: ENST00000397701.9_4
Gencode Gene: ENSG00000182362.14_7
Transcript (Including UTRs)
   Position: hg19 chr21:47,706,256-47,717,665 Size: 11,410 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr21:47,706,828-47,717,548 Size: 10,721 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:47,706,256-47,717,665)mRNA (may differ from genome)Protein (167 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: YBEY_HUMAN
DESCRIPTION: RecName: Full=rRNA maturation factor homolog;
FUNCTION: May have metal-dependent hydrolase activity (Potential).
COFACTOR: Binds 1 zinc ion (By similarity).
SUBCELLULAR LOCATION: Nucleus.
MISCELLANEOUS: A protein of the expected size has been detected by antibody binding and Western blot in at least one of the analyzed tissues or cells (PubMed:22042635).
SIMILARITY: Belongs to the rRNA maturation factor YbeY family.
SEQUENCE CAUTION: Sequence=AAK74138.1; Type=Erroneous translation; Note=Wrong choice of CDS; Sequence=AAK74139.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAK74140.1; Type=Erroneous translation; Note=Wrong choice of CDS; Sequence=AAK74141.1; Type=Erroneous translation; Note=Wrong choice of CDS;

-  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: 55.63 RPKM in Testis
Total median expression: 329.88 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -41.60118-0.353 Picture PostScript Text
3' UTR -45.30117-0.387 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
IPR023091 - MetalPrtase_cat_dom_prd
IPR020549 - UPF0054_CS
IPR002036 - UPF0054_metalloprotease_prd

Pfam Domains:
PF02130 - Endoribonuclease YbeY

SCOP Domains:
55486 - Metalloproteases ("zincins"), catalytic domain

ModBase Predicted Comparative 3D Structure on P58557
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 orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004222 metalloendopeptidase activity
GO:0004518 nuclease activity
GO:0004519 endonuclease activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006364 rRNA processing
GO:0006508 proteolysis
GO:0090305 nucleic acid phosphodiester bond hydrolysis

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK294975 - Homo sapiens cDNA FLJ50010 complete cds.
BC119770 - Homo sapiens chromosome 21 open reading frame 57, mRNA (cDNA clone MGC:148110 IMAGE:40108760), complete cds.
BC122865 - Homo sapiens chromosome 21 open reading frame 57, mRNA (cDNA clone MGC:148109 IMAGE:40108759), complete cds.
BC131553 - Homo sapiens chromosome 21 open reading frame 57, mRNA (cDNA clone MGC:148056 IMAGE:40089560), complete cds.
AY040873 - Homo sapiens C21orf57 isoform A protein (C21orf57) mRNA, partial cds, alternatively spliced.
AY040874 - Homo sapiens C21orf57 isoform B protein (C21orf57) mRNA, partial cds, alternatively spliced.
AY040875 - Homo sapiens C21orf57 isoform C protein (C21orf57) mRNA, partial cds, alternatively spliced.
AY040876 - Homo sapiens C21orf57 isoform D protein (C21orf57) mRNA, partial cds, alternatively spliced.
BC022828 - Homo sapiens chromosome 21 open reading frame 57, mRNA (cDNA clone MGC:39340 IMAGE:3928883), complete cds.
AK128875 - Homo sapiens cDNA FLJ46907 fis, clone FEBRA2000805.
BC068100 - Homo sapiens chromosome 21 open reading frame 57, mRNA (cDNA clone IMAGE:6379862), with apparent retained intron.
KJ894007 - Synthetic construct Homo sapiens clone ccsbBroadEn_03401 YBEY gene, encodes complete protein.
JD273487 - Sequence 254511 from Patent EP1572962.
JD200944 - Sequence 181968 from Patent EP1572962.
JD215256 - Sequence 196280 from Patent EP1572962.
JD057380 - Sequence 38404 from Patent EP1572962.
JD407103 - Sequence 388127 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B7WPA9, B7WPF7, C21orf57, D3DSN2, ENST00000397701.1, ENST00000397701.2, ENST00000397701.3, ENST00000397701.4, ENST00000397701.5, ENST00000397701.6, ENST00000397701.7, ENST00000397701.8, NM_001314025, P58557, uc318zfk.1, uc318zfk.2, YBEY_HUMAN
UCSC ID: ENST00000397701.9_4
RefSeq Accession: NM_001314025.2
Protein: P58557 (aka YBEY_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.