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Aliases for YBEY Gene

Aliases for YBEY Gene

  • YbeY Metallopeptidase (Putative) 2 3 5
  • C21orf57 3 4
  • Chromosome 21 Open Reading Frame 57 2
  • Putative Metalloprotease C21orf57 3
  • RRNA Maturation Factor Homolog 3
  • Endoribonuclease YbeY 3
  • Putative Ribonuclease 3
  • EC 3.1.-.- 4

External Ids for YBEY Gene

Previous HGNC Symbols for YBEY Gene

  • C21orf57

Previous GeneCards Identifiers for YBEY Gene

  • GC21P047707

Summaries for YBEY Gene

Entrez Gene Summary for YBEY Gene

  • This gene encodes a highly conserved metalloprotein. A similar protein in bacteria acts as an endoribonuclease, and is thought to function in ribosomal RNA maturation and ribosome assembly. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

GeneCards Summary for YBEY Gene

YBEY (YbeY Metallopeptidase (Putative)) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include metalloendopeptidase activity.

UniProtKB/Swiss-Prot for YBEY Gene

  • Single strand-specific metallo-endoribonuclease involved in rRNA maturation.

Additional gene information for YBEY Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for YBEY Gene

Genomics for YBEY Gene

GeneHancer (GH) Regulatory Elements for YBEY Gene

Promoters and enhancers for YBEY Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH21I046283 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 581.6 -0.7 -686 4.1 HDGF PKNOX1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B MCM3AP YBEY ENSG00000228137 DIP2A POFUT2 ENSG00000227438 MCM3AP-AS1 COL6A1 ENSG00000215447 SPATC1L
GH21I046294 Enhancer 1.4 Ensembl ENCODE dbSUPER 46.5 +10.1 10097 4.1 HDGF PKNOX1 ARID4B DMAP1 TCF12 POLR2B GLIS2 ATF7 SP3 NCOA1 YBEY MCM3AP DIP2A MCM3AP-AS1 ENSG00000228137 SPATC1L S100B GC21P046294 GC21P046292 C21orf58
GH21I046226 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 26.7 -57.9 -57916 4.9 HDGF PKNOX1 CLOCK MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B POLR2B MCM3AP-AS1 LSS MCM3AP YBEY SPATC1L ENSG00000228137 COL6A1 PIR60990
GH21I046319 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 25.1 +37.0 37019 6.7 CLOCK DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 C21orf58 PCNT ENSG00000228137 MCM3AP ENSG00000227438 MCM3AP-AS1 DIP2A SPATC1L YBEY COL6A1
GH21I046182 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 19.1 -102.2 -102228 4.1 HDGF PKNOX1 ATF1 ARNT ARID4B SIN3A ZBTB7B TCF12 POLR2B ZNF766 SPATC1L ENSG00000228404 MCM3AP YBEY MCM3AP-AS1 COL6A2 LOC105372842 ENSG00000228137 FTCD LSS
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around YBEY on UCSC Golden Path with GeneCards custom track

Genomic Locations for YBEY Gene

Genomic Locations for YBEY Gene
chr21:46,286,310-46,313,225
(GRCh38/hg38)
Size:
26,916 bases
Orientation:
Plus strand
chr21:47,706,251-47,717,665
(GRCh37/hg19)

Genomic View for YBEY Gene

Genes around YBEY on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
YBEY Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for YBEY Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for YBEY Gene

Proteins for YBEY Gene

  • Protein details for YBEY Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P58557-YBEY_HUMAN
    Recommended name:
    Endoribonuclease YbeY
    Protein Accession:
    P58557
    Secondary Accessions:
    • B7WPA9
    • B7WPF7
    • D3DSN2

    Protein attributes for YBEY Gene

    Size:
    167 amino acids
    Molecular mass:
    19298 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    No Data Available
    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.
    SequenceCaution:
    • Sequence=AAK74138.1; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305}; Sequence=AAK74139.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=AAK74140.1; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305}; Sequence=AAK74141.1; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305};

    Alternative splice isoforms for YBEY Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for YBEY Gene

Post-translational modifications for YBEY Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for YBEY Gene

Domains & Families for YBEY Gene

Gene Families for YBEY Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for YBEY Gene

Suggested Antigen Peptide Sequences for YBEY Gene

Graphical View of Domain Structure for InterPro Entry

P58557

UniProtKB/Swiss-Prot:

YBEY_HUMAN :
  • Belongs to the endoribonuclease YbeY family.
Family:
  • Belongs to the endoribonuclease YbeY family.
genes like me logo Genes that share domains with YBEY: view

Function for YBEY Gene

Molecular function for YBEY Gene

UniProtKB/Swiss-Prot Function:
Single strand-specific metallo-endoribonuclease involved in rRNA maturation.

Enzyme Numbers (IUBMB) for YBEY Gene

Phenotypes From GWAS Catalog for YBEY Gene

Gene Ontology (GO) - Molecular Function for YBEY Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004222 metalloendopeptidase activity IEA --
GO:0004518 nuclease activity IEA --
GO:0004519 endonuclease activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with YBEY: view
genes like me logo Genes that share phenotypes with YBEY: view

Animal Model Products

  • Taconic Biosciences Mouse Models for YBEY

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for YBEY Gene

Localization for YBEY Gene

Subcellular locations from UniProtKB/Swiss-Prot for YBEY Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for YBEY gene
Compartment Confidence
nucleus 5
mitochondrion 4
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for YBEY Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 22042635
GO:0005739 mitochondrion IEA --
genes like me logo Genes that share ontologies with YBEY: view

Pathways & Interactions for YBEY Gene

No Data Available

Gene Ontology (GO) - Biological Process for YBEY Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006364 rRNA processing IEA --
GO:0006508 proteolysis IEA --
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
genes like me logo Genes that share ontologies with YBEY: view

No data available for Pathways by source and SIGNOR curated interactions for YBEY Gene

Drugs & Compounds for YBEY Gene

No Compound Related Data Available

Transcripts for YBEY Gene

mRNA/cDNA for YBEY Gene

(17) REFSEQ mRNAs :
(12) Additional mRNA sequences :
(8) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for YBEY Gene

YbeY metallopeptidase (putative):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for YBEY Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7
SP1: - - - - -
SP2: - - - - - -
SP3: - - -
SP4: - - - -
SP5: - - - - - - -
SP6: - - - -
SP7: - - -
SP8: - -
SP9:

Relevant External Links for YBEY Gene

GeneLoc Exon Structure for
YBEY
ECgene alternative splicing isoforms for
YBEY

Expression for YBEY Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for YBEY Gene

mRNA differential expression in normal tissues according to GTEx for YBEY Gene

This gene is overexpressed in Testis (x5.6).

Protein differential expression in normal tissues from HIPED for YBEY Gene

This gene is overexpressed in Lung (49.7), Fetal ovary (10.2), and Testis (9.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for YBEY Gene



Protein tissue co-expression partners for YBEY Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of YBEY Gene:

YBEY

SOURCE GeneReport for Unigene cluster for YBEY Gene:

Hs.474066
genes like me logo Genes that share expression patterns with YBEY: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for YBEY Gene

Orthologs for YBEY Gene

This gene was present in the common ancestor of chordates.

Orthologs for YBEY Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia YBEY 33 34
  • 99.4 (n)
rat
(Rattus norvegicus)
Mammalia Ybey 33
  • 83.74 (n)
mouse
(Mus musculus)
Mammalia Ybey 33 16 34
  • 82.32 (n)
cow
(Bos Taurus)
Mammalia YBEY 33 34
  • 77.03 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia YBEY 34
  • 75 (a)
OneToOne
dog
(Canis familiaris)
Mammalia YBEY 33 34
  • 73.17 (n)
oppossum
(Monodelphis domestica)
Mammalia YBEY 34
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves YBEY 34
  • 57 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia YBEY 34
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ybey 33
  • 60.83 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100537917 33
  • 61.28 (n)
ybey 34 34
  • 59 (a)
OneToMany
wufb30h03 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2303 33
Species where no ortholog for YBEY was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for YBEY Gene

ENSEMBL:
Gene Tree for YBEY (if available)
TreeFam:
Gene Tree for YBEY (if available)

Paralogs for YBEY Gene

(1) SIMAP similar genes for YBEY Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with YBEY: view

No data available for Paralogs for YBEY Gene

Variants for YBEY Gene

Sequence variations from dbSNP and Humsavar for YBEY Gene

SNP ID Clin Chr 21 pos Variation AA Info Type
rs35902237 benign, not specified 46,302,072(+) TGGTGGTGGTGGTGGTGGTGGTG/TGGTGGTGGTGGTG/TGGTGGTGGTGGTGGTG/TGGTGGTGGTGGTGGTGGTG/TGGTGGTGGTGGTGGTGGTGGTGGTG/TGGTGGTGGTGGTGGTGGTGGTGGTGGTG genic_downstream_transcript_variant, intron_variant
rs58271568 benign, not specified 46,287,126(+) AAAAAAAAAA/AAAAAAAAAAAA/AAAAAAAAAAAAA/AAAAAAAAAAAAAA/AAAAAAAAAAAAAAA/AAAAAAAAAAAAAAAA/AAAAAAAAAAAAAAAAA genic_upstream_transcript_variant, intron_variant
rs61182475 benign, not specified 46,287,136(+) T/A genic_upstream_transcript_variant, intron_variant
rs9975588 benign, not specified 46,284,982(+) G/A upstream_transcript_variant
rs1000104642 -- 46,287,421(+) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for YBEY Gene

Variant ID Type Subtype PubMed ID
dgv2516e59 CNV duplication 20981092
dgv7929n54 CNV loss 21841781
esv1185684 CNV insertion 17803354
esv1190668 CNV deletion 17803354
esv2320022 CNV deletion 18987734
esv27873 CNV gain 19812545
esv9428 CNV gain 19470904
nsv1060978 CNV gain 25217958
nsv1110384 CNV duplication 24896259
nsv1142337 CNV tandem duplication 24896259
nsv3547 CNV insertion 18451855
nsv470910 CNV gain 18288195
nsv519904 CNV loss 19592680
nsv527355 CNV gain 19592680
nsv587975 CNV gain 21841781
nsv587977 CNV loss 21841781
nsv587980 CNV loss 21841781
nsv821184 CNV deletion 20802225

Variation tolerance for YBEY Gene

Residual Variation Intolerance Score: 47.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.22; 24.43% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for YBEY Gene

Human Gene Mutation Database (HGMD)
YBEY
SNPedia medical, phenotypic, and genealogical associations of SNPs for
YBEY

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for YBEY Gene

Disorders for YBEY Gene

Additional Disease Information for YBEY

No disorders were found for YBEY Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for YBEY Gene

Publications for YBEY Gene

  1. C21orf57 is a human homologue of bacterial YbeY proteins. (PMID: 28153719) Ghosal A … Walker GC (Biochemical and biophysical research communications 2017) 2 3 4 58
  2. Antibody-based protein profiling of the human chromosome 21. (PMID: 22042635) Uhlén M … Sivertsson Å (Molecular & cellular proteomics : MCP 2012) 3 4 58
  3. From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map. (PMID: 11707072) Reymond A … Antonarakis SE (Genomics 2001) 3 4 58
  4. The DNA sequence of human chromosome 21. (PMID: 10830953) Hattori M … Chromosome 21 mapping and sequencing consortium (Nature 2000) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for YBEY Gene

Sources for YBEY Gene

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