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YBEY ybeY metalloendoribonuclease [ Homo sapiens (human) ]

Gene ID: 54059, updated on 5-Mar-2024

Summary

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
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Genomic context

See YBEY in Genome Data Viewer
Location:
21q22.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (46286342..46313225)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (44668939..44699780)
105.20220307 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

Expression

  • 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

Related articles in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001006114.3NP_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:35113
    UPF0054; Uncharacterized protein family UPF0054
  2. NM_001314022.2NP_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:35106
    UPF0054; Uncharacterized protein family UPF0054
  3. NM_001314023.2NP_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:432
    SBDS_C; SBDS protein C-terminal domain
    cl00402
    Location:29104
    UPF0054; Uncharacterized protein family UPF0054
  4. NM_001314024.2NP_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:2761
    UPF0054; Uncharacterized protein family UPF0054
  5. NM_001314025.2NP_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:35149
    TIGR00043; rRNA maturation RNase YbeY
  6. NM_001314026.2NP_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:35113
    UPF0054; Uncharacterized protein family UPF0054
  7. NM_058181.3NP_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:35149
    TIGR00043; rRNA maturation RNase YbeY

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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_047440898.1XP_047296854.1  endoribonuclease YbeY isoform X3

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

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

    Conserved Domains (1) summary
    TIGR00043
    Location:35141
    TIGR00043; rRNA maturation RNase YbeY
  4. XM_047440897.1XP_047296853.1  endoribonuclease YbeY isoform X4

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

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

    Conserved Domains (1) summary
    TIGR00043
    Location:35141
    TIGR00043; rRNA maturation RNase YbeY
  7. XM_047440900.1XP_047296856.1  endoribonuclease YbeY isoform X5

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

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

  10. XM_011529635.3XP_011527937.1  endoribonuclease YbeY isoform X1

    See identical proteins and their annotated locations for XP_011527937.1

    Conserved Domains (1) summary
    TIGR00043
    Location:35141
    TIGR00043; rRNA maturation RNase YbeY
  11. XM_011529630.3XP_011527932.1  endoribonuclease YbeY isoform X1

    See identical proteins and their annotated locations for XP_011527932.1

    Conserved Domains (1) summary
    TIGR00043
    Location:35141
    TIGR00043; rRNA maturation RNase YbeY
  12. XM_011529629.3XP_011527931.1  endoribonuclease YbeY isoform X1

    See identical proteins and their annotated locations for XP_011527931.1

    Conserved Domains (1) summary
    TIGR00043
    Location:35141
    TIGR00043; rRNA maturation RNase YbeY
  13. XM_047440902.1XP_047296858.1  endoribonuclease YbeY isoform X6

    UniProtKB/Swiss-Prot
    B7WPA9, B7WPF7, D3DSN2, P58557
    Related
    ENSP00000380805.1, ENST00000397691.1
  14. XM_047440903.1XP_047296859.1  endoribonuclease YbeY isoform X8

  15. XM_005261156.5XP_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_054324658.1XP_054180633.1  endoribonuclease YbeY isoform X3

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

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

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

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

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

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

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

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

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

    UniProtKB/Swiss-Prot
    B7WPA9, B7WPF7, D3DSN2, P58557
  11. XM_054324661.1XP_054180636.1  endoribonuclease YbeY isoform X5

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

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