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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
  • Putative Ribonuclease 3

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. GO annotations related to this gene include metalloendopeptidase activity.

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

Genomics for YBEY Gene

Regulatory Elements for YBEY Gene

Enhancers for YBEY Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH21G046294 1.5 Ensembl ENCODE dbSUPER 46.4 +10.1 10098 4.1 HDGF PKNOX1 AGO1 ARID4B DMAP1 TCF12 GLIS2 SP3 MXD4 NFYC YBEY MCM3AP SPATC1L DIP2A S100B GC21P046294 GC21P046292 C21orf58
GH21G046283 1.2 ENCODE 31.5 -0.7 -687 4.1 HDGF PKNOX1 CREB3L1 ARNT AGO1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 MCM3AP YBEY ENSG00000228137 ENSG00000227438 SPATC1L LSS GC21M046276 PIR54929
GH21G046319 1.4 ENCODE dbSUPER 25.1 +37.0 37020 6.7 CREB3L1 AGO1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZNF610 GLIS1 MCM3AP-AS1 MCM3AP ENSG00000228137 SPATC1L YBEY ENSG00000227438 DSTNP1 LSS ENSG00000223901 LOC105372842
GH21G046226 1.3 ENCODE dbSUPER 26.7 -57.9 -57916 4.9 HDGF PKNOX1 MLX CREB3L1 AGO1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YBEY SPATC1L MCM3AP-AS1 MCM3AP LSS PIR60990
GH21G046187 1.5 Ensembl ENCODE dbSUPER 19.3 -96.6 -96606 4.5 HDGF PKNOX1 ATF1 SIN3A ZNF48 FOS ZNF263 CAVIN1 ZHX2 JUNB MCM3AP YBEY SPATC1L MCM3AP-AS1 FTCD ENSG00000223901
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around YBEY on UCSC Golden Path with GeneCards custom track

Promoters for YBEY Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000143372 -10 1801 PKNOX1 CREB3L1 ARNT AGO1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 CBX5

Genomic Location for YBEY Gene

Chromosome:
21
Start:
46,286,310 bp from pter
End:
46,313,225 bp from pter
Size:
26,916 bases
Orientation:
Plus strand

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:
    Putative ribonuclease
    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

No Post-translational modifications

No data available for DME Specific Peptides for YBEY Gene

Domains & Families for YBEY Gene

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

No data available for Gene Families for YBEY Gene

Function 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: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

CRISPR Products

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , 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

Gene Ontology (GO) - Cellular Components for YBEY Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 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 --
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

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 34 35
  • 99.4 (n)
rat
(Rattus norvegicus)
Mammalia Ybey 34
  • 83.74 (n)
mouse
(Mus musculus)
Mammalia Ybey 34 16 35
  • 82.32 (n)
cow
(Bos Taurus)
Mammalia YBEY 34 35
  • 77.03 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia YBEY 35
  • 75 (a)
OneToOne
dog
(Canis familiaris)
Mammalia YBEY 34 35
  • 73.17 (n)
oppossum
(Monodelphis domestica)
Mammalia YBEY 35
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves YBEY 35
  • 57 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia YBEY 35
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ybey 34
  • 60.83 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100537917 34
  • 61.28 (n)
ybey 35 35
  • 59 (a)
OneToMany
wufb30h03 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2303 34
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 Sequence Context AA Info Type
rs1000104642 -- 46,287,421(+) TGCTC(C/T)TGAAC intron-variant, upstream-variant-2KB
rs1000292264 -- 46,303,290(+) GCCAT(C/G)ATCAT intron-variant
rs1000410052 -- 46,300,076(+) GGCCA(C/T)CCAAA intron-variant, downstream-variant-500B, utr-variant-3-prime
rs1000470171 -- 46,298,234(+) AGGGA(C/T)ATGAA intron-variant, downstream-variant-500B, utr-variant-3-prime
rs1000642637 -- 46,303,610(+) ACTTT(A/G)GGAGA 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)

Relevant External Links for YBEY Gene

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

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

Disorders for YBEY Gene

Relevant External Links for YBEY

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 G.C. (Biochem. Biophys. Res. Commun. 2017) 2 3 64
  2. Antibody-based protein profiling of the human chromosome 21. (PMID: 22042635) Uhlen M. … Sivertsson A. (Mol. Cell. Proteomics 2012) 3 4 64
  3. From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map. (PMID: 11707072) Reymond A. … Antonarakis S.E. (Genomics 2001) 3 4 64
  4. The DNA sequence of human chromosome 21. (PMID: 10830953) Hattori M. … Yaspo M.-L. (Nature 2000) 3 4 64
  5. Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function. (PMID: 27499296) Floyd B.J. … Pagliarini D.J. (Mol. Cell 2016) 3 64

Products for YBEY Gene

Sources for YBEY Gene

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