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    YBEY ybeY metalloendoribonuclease [ Homo sapiens (human) ]

    Gene ID: 54059, updated on 28-Oct-2024

    Summary

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    Official Symbol
    YBEYprovided by HGNC
    Official Full Name
    ybeY metalloendoribonucleaseprovided by HGNC
    Primary source
    HGNC:HGNC:1299
    See related
    Ensembl:ENSG00000182362 MIM:617461; AllianceGenome:HGNC:1299
    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
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    Genomic context

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    See YBEY in Genome Data Viewer
    Location:
    21q22.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (46286342..46313225)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (44668939..44699780)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (47706256..47717665)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47614165-47614666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47614667-47615166 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47621241-47621767 Neighboring gene small nucleolar RNA, C/D box 159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47638552-47639452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47640419-47640920 Neighboring gene lanosterol synthase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18598 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13413 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13414 Neighboring gene Sharpr-MPRA regulatory region 3947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13416 Neighboring gene MCM3AP antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18599 Neighboring gene minichromosome maintenance complex component 3 associated protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13417 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13418 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:47709143-47709725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:47709726-47710307 Neighboring gene Sharpr-MPRA regulatory region 4411 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47715289-47715862 Neighboring gene Sharpr-MPRA regulatory region 1466 Neighboring gene chromosome 21 open reading frame 58 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47736113-47736948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47737784-47738618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47738619-47739453 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:47741059-47741321 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18600 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13419 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13420 Neighboring gene uncharacterized LOC128092249 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:47746938-47747110 Neighboring gene pericentrin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18601 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47783310-47783810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18603 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47798693-47799473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47805909-47806409 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47823360-47823870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47823871-47824380 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47831521-47832096 Neighboring gene ribosomal protein L18a pseudogene 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    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, éminence grise of ribosome biogenesis. Liao Z, et al. Biochem Soc Trans, 2021 Apr 30. PMID 33929506
    3. YBEY is an essential biogenesis factor for mitochondrial ribosomes. Summer S, et al. Nucleic Acids Res, 2020 Sep 25. PMID 32182356, Free PMC Article
    4. 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
    5. Antibody-based protein profiling of the human chromosome 21. Uhlén M, et al. Mol Cell Proteomics, 2012 Mar. PMID 22042635, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. YbeY, eminence grise of ribosome biogenesis.
      Title: YbeY, éminence grise of ribosome biogenesis.
    2. 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.
    3. YBEY is an essential biogenesis factor for mitochondrial ribosomes.
      Title: YBEY is an essential biogenesis factor for mitochondrial ribosomes.
    4. 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.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    Submit: New GeneRIF Correction

    Phenotypes

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

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See Variation Viewer (GRCh37.p13)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ46907

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA endonuclease 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 rRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrion HTP PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    endoribonuclease YbeY
    Names
    putative metalloprotease C21orf57
    putative ribonuclease
    rRNA maturation factor homolog
    ybeY metallopeptidase (putative)

    NCBI Reference Sequences (RefSeq)

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    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
      B7WPA9, B7WPF7, D3DSN2, 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/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
      B7WPA9, B7WPF7, D3DSN2, P58557
      Related
      ENSP00000329614.3, ENST00000329319.7
      Conserved Domains (1) summary
      TIGR00043
      Location:35 → 149
      TIGR00043; rRNA maturation RNase YbeY

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      46286342..46313225
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440898.1 → XP_047296854.1  endoribonuclease YbeY isoform X3

    2. XM_047440901.1 → XP_047296857.1  endoribonuclease YbeY isoform X4

    3. XM_011529633.3 → XP_011527935.1  endoribonuclease YbeY isoform X3

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

    4. XM_047440897.1 → XP_047296853.1  endoribonuclease YbeY isoform X4

    5. XM_017028394.2 → XP_016883883.2  endoribonuclease YbeY isoform X7

    6. XM_011529631.3 → XP_011527933.1  endoribonuclease YbeY isoform X2

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

    7. XM_047440900.1 → XP_047296856.1  endoribonuclease YbeY isoform X5

    8. XM_047440899.1 → XP_047296855.1  endoribonuclease YbeY isoform X5

    9. XM_011529634.3 → XP_011527936.3  endoribonuclease YbeY isoform X5

    10. XM_011529635.3 → 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

    11. XM_011529630.3 → 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

    12. XM_011529629.3 → 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

    13. XM_047440902.1 → XP_047296858.1  endoribonuclease YbeY isoform X6

      UniProtKB/Swiss-Prot
      B7WPA9, B7WPF7, D3DSN2, P58557
      Related
      ENSP00000380805.1, ENST00000397691.1

    14. XM_047440903.1 → XP_047296859.1  endoribonuclease YbeY isoform X8

    15. XM_005261156.5 → XP_005261213.3  endoribonuclease YbeY isoform X8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      44668939..44699780
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324658.1 → XP_054180633.1  endoribonuclease YbeY isoform X3

    2. XM_054324662.1 → XP_054180637.1  endoribonuclease YbeY isoform X4

    3. XM_054324659.1 → XP_054180634.1  endoribonuclease YbeY isoform X3

    4. XM_054324663.1 → XP_054180638.1  endoribonuclease YbeY isoform X4

    5. XM_054324665.1 → XP_054180640.1  endoribonuclease YbeY isoform X7

    6. XM_054324657.1 → XP_054180632.1  endoribonuclease YbeY isoform X2

    7. XM_054324660.1 → XP_054180635.1  endoribonuclease YbeY isoform X5

    8. XM_054324655.1 → XP_054180630.1  endoribonuclease YbeY isoform X1

    9. XM_054324666.1 → XP_054180641.1  endoribonuclease YbeY isoform X8

    10. XM_054324664.1 → XP_054180639.1  endoribonuclease YbeY isoform X6

      UniProtKB/Swiss-Prot
      B7WPA9, B7WPF7, D3DSN2, P58557

    11. XM_054324661.1 → XP_054180636.1  endoribonuclease YbeY isoform X5

    12. XM_054324656.1 → XP_054180631.1  endoribonuclease YbeY isoform X1

    13. XM_054324667.1 → XP_054180642.1  endoribonuclease YbeY isoform X8

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

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