Sign in to NCBI
Format

Send to:

Choose Destination

YBEY ybeY metalloendoribonuclease [ Homo sapiens (human) ]

Gene ID: 54059, updated on 28-Jun-2021

Summary

Go to the top of the page Help
Official Symbol
YBEYprovided by HGNC
Official Full Name
ybeY metalloendoribonucleaseprovided by HGNC
Primary source
HGNC:HGNC:1299
See related
Ensembl:ENSG00000182362 MIM:617461
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
C21orf57
Summary
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]
Expression
Broad expression in testis (RPKM 8.0), thyroid (RPKM 5.5) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See YBEY in Genome Data Viewer
Location:
21q22.3
Exon count:
10
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 21 NC_000021.9 (46286056..46314188)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (47706256..47717665)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 3947 Neighboring gene MCM3AP antisense RNA 1 Neighboring gene minichromosome maintenance complex component 3 associated protein Neighboring gene Sharpr-MPRA regulatory region 1466 Neighboring gene chromosome 21 open reading frame 58 Neighboring gene pericentrin Neighboring gene ribosomal protein L18a pseudogene 2 Neighboring gene DIP2A intronic transcript 1 Neighboring gene disco interacting protein 2 homolog A

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. YbeY is required for ribosome small subunit assembly and tRNA processing in human mitochondria. D'Souza AR, et al. Nucleic Acids Res, 2021 Jun 4. PMID 34037799, Free PMC Article
  2. YBEY is an essential biogenesis factor for mitochondrial ribosomes. Summer S, et al. Nucleic Acids Res, 2020 Sep 25. PMID 32182356, Free PMC Article
  3. C21orf57 is a human homologue of bacterial YbeY proteins. Ghosal A, et al. Biochem Biophys Res Commun, 2017 Mar 11. PMID 28153719, Free PMC Article
  4. Antibody-based protein profiling of the human chromosome 21. Uhlén M, et al. Mol Cell Proteomics, 2012 Mar. PMID 22042635, Free PMC Article
  5. From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map. Reymond A, et al. Genomics, 2001 Nov. PMID 11707072

See all (21) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. YbeY is required for ribosome small subunit assembly and tRNA processing in human mitochondria.
    Title: YbeY is required for ribosome small subunit assembly and tRNA processing in human mitochondria.
  2. YBEY is an essential biogenesis factor for mitochondrial ribosomes.
    Title: YBEY is an essential biogenesis factor for mitochondrial ribosomes.
  3. This observation suggests that the function of HuYbeY in human cells is likely regulated through specific interactions with partner proteins similarly to the way YbeY is regulated in bacteria.
    Title: C21orf57 is a human homologue of bacterial YbeY proteins.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • FLJ46907

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables endoribonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables metalloendopeptidase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in RNA phosphodiester bond hydrolysis, endonucleolytic IEA
Inferred from Electronic Annotation
more info
  
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
  
involved_in rRNA processing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
endoribonuclease YbeY
Names
putative metalloprotease C21orf57
putative ribonuclease
rRNA maturation factor homolog
ybeY metallopeptidase (putative)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001006114.3 → NP_001006114.1  endoribonuclease YbeY isoform 2

    See identical proteins and their annotated locations for NP_001006114.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks two 3' exons, and its 3' terminal exon extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 2 and 7 encode the same isoform.
    Source sequence(s)
    AK294975, AP000471, DC384882
    UniProtKB/TrEMBL
    Q8TBC8
    Conserved Domains (1) summary
    cl00402
    Location:35 → 113
    UPF0054; Uncharacterized protein family UPF0054

  2. NM_001314022.2 → NP_001300951.1  endoribonuclease YbeY isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate, in-frame exon in the central coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AP000471, AY040874, DC384882
    Consensus CDS
    CCDS82687.1
    UniProtKB/Swiss-Prot
    P58557
    Related
    ENSP00000340675.6, ENST00000339195.10
    Conserved Domains (1) summary
    cl00402
    Location:35 → 106
    UPF0054; Uncharacterized protein family UPF0054

  3. NM_001314023.2 → NP_001300952.1  endoribonuclease YbeY isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AP000471, AY040875, DC384882
    Consensus CDS
    CCDS82685.1
    UniProtKB/Swiss-Prot
    P58557
    Related
    ENSP00000380808.1, ENST00000397694.5
    Conserved Domains (2) summary
    pfam09377
    Location:4 → 32
    SBDS_C; SBDS protein C-terminal domain
    cl00402
    Location:29 → 104
    UPF0054; Uncharacterized protein family UPF0054

  4. NM_001314024.2 → NP_001300953.1  endoribonuclease YbeY isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, uses an alternate in-frame splice site, and lacks an alternate in-frame exon in the coding region, compared to variant 1. The encoded isoform (5) is shorter than isoform 1.
    Source sequence(s)
    AP000471, AY040876, DC384882
    Consensus CDS
    CCDS82686.1
    UniProtKB/Swiss-Prot
    P58557
    Related
    ENSP00000380806.1, ENST00000397692.5
    Conserved Domains (1) summary
    cl00402
    Location:27 → 61
    UPF0054; Uncharacterized protein family UPF0054

  5. NM_001314025.2 → NP_001300954.1  endoribonuclease YbeY isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1. Variants 1 and 6 encode the same isoform (1).
    Source sequence(s)
    AK128875, AP000471, AY040874, DC384882
    Consensus CDS
    CCDS33591.1
    UniProtKB/Swiss-Prot
    P58557
    Related
    ENSP00000380813.4, ENST00000397701.9
    Conserved Domains (1) summary
    TIGR00043
    Location:35 → 149
    TIGR00043; rRNA maturation RNase YbeY

  6. NM_001314026.2 → NP_001300955.1  endoribonuclease YbeY isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks two 3' exons, and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 2 and 7 encode the same isoform.
    Source sequence(s)
    AK294975, AY040873, BC068100, DC384882
    UniProtKB/Swiss-Prot
    P58557
    UniProtKB/TrEMBL
    Q8TBC8
    Conserved Domains (1) summary
    cl00402
    Location:35 → 113
    UPF0054; Uncharacterized protein family UPF0054

  7. NM_058181.3 → NP_478061.1  endoribonuclease YbeY isoform 1

    See identical proteins and their annotated locations for NP_478061.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AP000471, AY040873, BG473705, DC384882
    Consensus CDS
    CCDS33591.1
    UniProtKB/Swiss-Prot
    P58557
    Related
    ENSP00000329614.3, ENST00000329319.7
    Conserved Domains (1) summary
    TIGR00043
    Location:35 → 149
    TIGR00043; rRNA maturation RNase YbeY

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p13 Primary Assembly

    Range
    46286056..46314188
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028394.1 → XP_016883883.1  endoribonuclease YbeY isoform X5

  2. XM_011529634.2 → XP_011527936.2  endoribonuclease YbeY isoform X4

  3. XM_005261156.4 → XP_005261213.2  endoribonuclease YbeY isoform X6

  4. XM_011529633.2 → XP_011527935.1  endoribonuclease YbeY isoform X3

    Conserved Domains (1) summary
    TIGR00043
    Location:35 → 141
    TIGR00043; rRNA maturation RNase YbeY

  5. XM_011529631.2 → XP_011527933.1  endoribonuclease YbeY isoform X2

    Conserved Domains (1) summary
    TIGR00043
    Location:35 → 141
    TIGR00043; rRNA maturation RNase YbeY

  6. XM_011529629.2 → XP_011527931.1  endoribonuclease YbeY isoform X1

    See identical proteins and their annotated locations for XP_011527931.1

    Conserved Domains (1) summary
    TIGR00043
    Location:35 → 141
    TIGR00043; rRNA maturation RNase YbeY

  7. XM_017028396.1 → XP_016883885.1  endoribonuclease YbeY isoform X8

    UniProtKB/TrEMBL
    Q8TBC8
    Conserved Domains (1) summary
    cl00402
    Location:35 → 113
    UPF0054; Uncharacterized protein family UPF0054

  8. XM_011529630.2 → XP_011527932.1  endoribonuclease YbeY isoform X1

    See identical proteins and their annotated locations for XP_011527932.1

    Conserved Domains (1) summary
    TIGR00043
    Location:35 → 141
    TIGR00043; rRNA maturation RNase YbeY

  9. XM_011529635.2 → XP_011527937.1  endoribonuclease YbeY isoform X1

    See identical proteins and their annotated locations for XP_011527937.1

    Conserved Domains (1) summary
    TIGR00043
    Location:35 → 141
    TIGR00043; rRNA maturation RNase YbeY

  10. XM_017028395.2 → XP_016883884.1  endoribonuclease YbeY isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P58557.2 GenPept UniProtKB/Swiss-Prot:P58557

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous
You are here: NCBI > Genes & Expression > Gene
Support Center