YBEY ybeY metalloendoribonuclease [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

Location:: 21q22.3

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	21	NC_000021.9 (46286342..46313225)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	21	NC_060945.1 (44668939..44683111)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	21	NC_000021.8 (47706256..47717665)

Chromosome 21 - NC_000021.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

YbeY, eminence grise of ribosome biogenesis.
Title: YbeY, éminence grise of ribosome biogenesis.
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.
YBEY is an essential biogenesis factor for mitochondrial ribosomes.
Title: YBEY is an essential biogenesis factor for mitochondrial ribosomes.
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.
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 variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-87728 (e-PCR)
- UniSTS:82028

SHGC-52108 (e-PCR)
- UniSTS:68090

Homology

Homologs of the YBEY gene: The YBEY gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, zebrafish, and frog.
Orthologs from Annotation Pipeline: 300 organisms have orthologs with human gene YBEY
Orthologs

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 RNA phosphodiester bond hydrolysis, endonucleolytic	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

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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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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)

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
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
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
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
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

D3DSN2, P58557

Related

ENSP00000380813.4, ENST00000397701.9

Conserved Domains (1) summary

TIGR00043
Location:35 → 149

TIGR00043; rRNA maturation RNase YbeY
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
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

D3DSN2, P58557

Related

ENSP00000329614.3, ENST00000329319.7

Conserved Domains (1) summary

TIGR00043
Location:35 → 149

TIGR00043; rRNA maturation RNase YbeY