FlyBase Gene Report: Dmel\Nop60B

General Information

Symbol

Dmel\Nop60B

Species

D. melanogaster

Name

Nucleolar protein at 60B

Annotation Symbol

CG3333

Feature Type

protein_coding_gene

FlyBase ID

FBgn0259937

Gene Model Status

Current

Stock Availability

14 publicly available

Gene Summary

Nucleolar protein at 60B (Nop60B) encodes a pseudouridine synthase that is a core component of H/ACA small nucleolar ribonucleoproteins (snoRNPs) and small Cajal body-specific ribonucleoproteins (scaRNPs). It is involved in pseudouridylation of cellular RNA, ribosome biogenesis, translation efficiency, cell proliferation, stress response and stem cell maintenance. [Date last reviewed: 2019-02-28] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

mfl, minifly, Uhg6

Key Links

Genomic Location

Cytogenetic map

60C1-60C2

Sequence location

2R:24,174,877..24,186,343 [+]

Recombination map

2-106

RefSeq locus

NT_033778 REGION:24174877..24186343

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (15 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables pseudouridine synthase activity

inferred from electronic annotation with InterPro:IPR020103

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN000565614

(GO Reference Genome Project, 2011-)

enables RNA binding

inferred from electronic annotation with InterPro:IPR020103, InterPro:IPR036974

(InterPro Project Members, 2004-)

inferred from electronic annotation with InterPro:IPR002478, InterPro:IPR020103, InterPro:IPR036974

(InterPro Project Members, 2004-)

Biological Process (11 terms)

Terms Based on Experimental Evidence (5 terms)

CV Term

Evidence

References

involved_in germ cell development

inferred from mutant phenotype

(Kauffman et al., 2003)

involved_in pseudouridine synthesis

inferred from mutant phenotype

(Giordano et al., 1999)

involved_in ribosome biogenesis

inferred from mutant phenotype

(Breznak et al., 2023, Giordano et al., 1999)

involved_in rRNA processing

inferred from mutant phenotype

(Giordano et al., 1999)

involved_in wing disc development

inferred from mutant phenotype

(Tortoriello et al., 2010)

Terms Based on Predictions or Assertions (7 terms)

CV Term

Evidence

References

involved_in box H/ACA sno(s)RNA 3'-end processing

inferred from biological aspect of ancestor with PANTHER:PTN000565614

(GO Reference Genome Project, 2011-)

involved_in mRNA pseudouridine synthesis

inferred from biological aspect of ancestor with PANTHER:PTN000565614

(GO Reference Genome Project, 2011-)

involved_in pseudouridine synthesis

inferred from electronic annotation with InterPro:IPR020103

(InterPro Project Members, 2004-)

involved_in RNA modification

inferred from electronic annotation with InterPro:IPR020103

(InterPro Project Members, 2004-)

involved_in RNA processing

inferred from electronic annotation with InterPro:IPR002501, InterPro:IPR004802

(InterPro Project Members, 2004-)

involved_in rRNA pseudouridine synthesis

inferred from biological aspect of ancestor with PANTHER:PTN000565614

(GO Reference Genome Project, 2011-)

involved_in snRNA pseudouridine synthesis

inferred from biological aspect of ancestor with PANTHER:PTN000565614

(GO Reference Genome Project, 2011-)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

is_active_in nucleolus

inferred from direct assay

(Breznak et al., 2023, Giordano et al., 1999)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of box H/ACA snoRNP complex

traceable author statement

(Breznak et al., 2023)

inferred from biological aspect of ancestor with PANTHER:PTN000565615

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

H/ACA SMALL NUCLEOLAR RIBONUCLEOPROTEIN COMPLEX

PSEUDOURIDINE SYNTHASES

Protein Family (UniProt)

Belongs to the pseudouridine synthase TruB family. (O44081)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

pseudouridine synthase activity
RHEA 48348:

Summaries

Gene Snapshot

Gene Group (FlyBase)

H/ACA SMALL NUCLEOLAR RIBONUCLEOPROTEIN COMPLEX -: H/ACA small nucleolar ribonucleoprotein complex (H/ACA snoRNP) is a ribosome processing complex that catalyzes pseudouridylation of ribosomal RNA (rRNA) residues. The H/ACA sRNP complex is composed of four different core proteins that assemble onto a H/ACA guide RNA scaffold which identify target uridines in the rRNA for modification during ribosome synthesis. (Adapted from PMID:22065625, FBrf0239135 and FBrf0161482).
PSEUDOURIDINE SYNTHASES -: Pseudouridine synthases catalyze the site-specific isomerization of uridine residues that are already part of an RNA chain, which is the most abundant post-transcriptional modification of cellular RNAs. Their activity is specific for a particular RNA (e.g. tRNA or rRNA class). They can be classified into five families named after the E. coli enzymes RluA, RsuA, TruA, TruB, and TruD. (Adapted from PMID:17113994.)

Protein Function (UniProtKB)

Catalytic subunit of the box H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA (PubMed:10087258, PubMed:37343092). This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1 (Probable). Pseudouridine ('psi') residues may serve to stabilize the conformation of rRNAs (Probable). Required for ribosome biogenesis; plays a central role in ribosomal RNA processing (PubMed:10087258, PubMed:37343092). H/ACA snoRNP complex-dependent ribosome biogenesis is important in female germline cell differentiation during oogenesis (PubMed:37343092). Essential for viability and female fertility (PubMed:10087258). Required for maintenance of the germline stem cell lineage during spermatogenesis (PubMed:12645924).

(UniProt, O44081)

Summary (Interactive Fly)

pseudouridylate synthase - enzymatically modifies ribosomal RNA - required for maintenance of germ-line stem cells

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Nop60B for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)

Isoform displayed:

Pfam protein domains

InterPro name

classification

start

end

Protein Domains (via SMART)

Isoform displayed:

SMART protein domains

InterPro name

classification

start

end

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry O44081)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

This is a fused gene: the 3' end corresponds to the non-coding gene Uhg6, which contains one or more snoRNA loci within intronic regions.

Gene model reviewed during 5.42

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.48

Possible mutation in sequenced strain; transposable element after first alternative polyadenylation site may inhibit alternative 3' UTR formation containing downstream snoRNA precursor sequence (Uhg6).

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Nop60B-RA

FBtr0072258

NM_080381

1753

508

Nop60B-RB

FBtr0100213

NM_001014547

2218

508

Nop60B-RC

FBtr0300227

NM_001169815

2184

508

Nop60B-RF

FBtr0300861

NM_001169818

3412

508

Nop60B-RG

FBtr0304599

NM_001259561

971

227

Additional Transcript Data and Comments

Reported size (kB)

2.0, 1.8 (northern blot)

(Giordano et al., 1999)

~1.5 (northern blot); 1.7 (longest cDNA)

(Phillips et al., 1998)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

Nop60B-PA

FBpp0072166

56.8

508

9.88

FBpp0099583

56.8

508

9.88

FBpp0289464

56.8

508

9.88

FBpp0290083

56.8

508

9.88

FBpp0293141

25.8

227

10.38

A0A0B4K8B2

NP_001246490

AFH08243

Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

508 aa isoforms: Nop60B-PA, Nop60B-PB, Nop60B-PC, Nop60B-PF

Additional Polypeptide Data and Comments

Reported size (kDa)

508 (aa); 56 (kD predicted)

(Giordano et al., 1999)

508 (aa)

(Phillips et al., 1998)

Comments

Nop60B protein rescues the function of the yeast cbf5 gene.

(Phillips et al., 1998)

External Data

Subunit Structure (UniProtKB)

Component of the box H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex consisting of Nop60B, Gar1, NPH2 and Nop10, and associated with H/ACA-type snoRNAs.

(UniProt, O44081)

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Nop60B using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Nop60B_1

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.39

Transcript Expression

No Assay Recorded

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

(Giordano et al., 1999)

embryonic stage 4 -- 14

organism | ubiquitous

(Phillips et al., 1998)

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

organism | ubiquitous

(Phillips et al., 1998)

embryonic stage -- adult stage

(Giordano et al., 1999)

embryonic stage 1 -- 9

Comment: reference states 0-4 hr AEL

(Giordano et al., 1999)

oogenesis stage S3 -- S14 & adult stage | female

nurse cell

(Phillips et al., 1998)

oocyte

(Phillips et al., 1998)

oogenesis

ovary | ubiquitous

(Phillips et al., 1998)

ovary

(Giordano et al., 1999)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage & larval stage

(Giordano et al., 1999)

embryonic stage 1 -- 9

Comment: reference states 0-4 hr AEL

(Giordano et al., 1999)

embryonic stage 1 -- 11

Comment: reference states 0-6 hr AEL

(Giordano et al., 1999)

adult stage | female

(Giordano et al., 1999)

adult stage & oogenesis

nurse cell

(Giordano et al., 1999)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

No Assay Recorded

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

organism | ubiquitous

(Phillips et al., 1998)

oogenesis

ovary

(Giordano et al., 1999)

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

organism | ubiquitous

(Phillips et al., 1998)

third instar larval stage

wing disc | ubiquitous

• nucleolus

(Tortoriello et al., 2010)

adult stage & oogenesis

germarium

(Phillips et al., 1998)

follicle cell

(Phillips et al., 1998)

oogenesis

organism | ubiquitous

(Phillips et al., 1998)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

Nop60B protein is localized to the nucleolus during interphase. During mitosis the protein is localized throughout the cytoplasm and is absent from the condensed chromosomes. With confocal microscopy, a low level of punctate nuclear staining is seen in addition to the nucleolar staining.

(Phillips et al., 1998)

High levels of Nop60B protein are observed in the germarium but not in the nurse cells or oocyte at later stages. Abundant Nop60B protein is evident in follicle cells. Nop60B protein is found throughout the embryo.

(Phillips et al., 1998)

Marker for

Subcellular Localization

CV Term

Evidence

References

is_active_in nucleolus

inferred from direct assay

(Breznak et al., 2023, Giordano et al., 1999)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Nop60B in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\Nop60B

View exonic expression by tissue for Dmel\Nop60B

Bulk Downloads

RNA-Seq RPKM values for all genes

Reference

See Gelbart and Emmert, 2013 for analysis details and data files for all genes.

Developmental Proteome: Life Cycle

Developmental Proteome: Embryogenesis

External Data and Images

Linkouts

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

37873/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0259937

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0259937

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG3333

Flygut - An atlas of the Drosophila adult midgut

FBgn0259937

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 16 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 13 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Nop60B

Transgenic constructs containing regulatory region of Nop60B

Aberrations (Deficiencies and Duplications) ( 6 )

Inferred from experimentation ( 6 )

Gene disrupted in

Df(2R)BSC155

(Christensen and Cook, 2006.5.11)

Df(2R)Exel6081

(Ryder, 2004.4.26)

Df(2R)Exel7184

(Ryder, 2004.4.26)

In(2LR)Px⁴

(Kauffman et al., 2003, Giordano et al., 1999, Spradling et al., 1999, Phillips et al., 1998, BDGP Project Members, 1994-1999)

Gene not disrupted in

Df(2R)bw^VDe2LPx^KR

(Spradling et al., 1999, Beaton, 1997.12.27)

Df(2R)Px2

(Kauffman et al., 2003, Spradling et al., 1999, BDGP Project Members, 1994-1999)

Inferred from location ( 3 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal

lethal, with Scer\GAL4^Act5C.PI

Nop60B^RNAi.sp.UAS

lethal, with Scer\GAL4^insc-Mz1407

lethal | recessive

lethal - all die before end of larval stage, with Scer\GAL4^Act5C.PU

Nop60B^GD16822

lethal - all die before end of larval stage, with Scer\GAL4^ap-md544

Nop60B^GD16822

lethal - all die before end of larval stage | recessive

lethal - all die before end of pupal stage | recessive

Nop60B^k06308

lethal - all die during embryonic stage | recessive

lethal - all die during P-stage, with Scer\GAL4^Mef2.PR

Nop60B^GD16822

partially lethal - majority die, with Scer\GAL4^pnr-MD237

Nop60B^GD10940

viable

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Nop60B^GD10940

viable, with Scer\GAL4^pnr-MD237

Nop60B^GD16822

viable, with Scer\GAL4^tin.CΔ4

Sterility

Allele

female semi-fertile, with Scer\GAL4^Act5C.PI

Nop60B^RNAi.Sym.UAS

female semi-sterile | recessive

Nop60B¹

female sterile, with Scer\GAL4^nanos.PG

male sterile

male sterile (with Nop60B^DL2011)

Nop60B^mM176

male sterile (with Nop60B^mM176)

Nop60B^DL2011

sterile

Nop60B^DL2011

sterile (with In(2LR)Px⁴)

Nop60B^DL2011

sterile (with Nop60B^DL3)

Nop60B^DL2011

sterile (with Nop60B^DL4)

Nop60B^DL2011

sterile (with Nop60B^DL6)

Nop60B^DL2011

sterile (with Nop60B^DL10)

Nop60B^DL2011

sterile (with Nop60B^DL2011)

Other Phenotypes

Allele

abnormal developmental rate, with Scer\GAL4^Act5C.PI

Nop60B^RNAi.Sym.UAS

abnormal developmental rate | recessive

Nop60B¹

abnormal neuroanatomy | larval stage, with Scer\GAL4^insc-Mz1407

decreased body size | larval stage | recessive

decreased cell size, with Scer\GAL4^nub-AC-62

Nop60B^GD16822

decreased fecundity, with Scer\GAL4^nanos.PG

Nop60B^GL00555

decreased occurrence of cell division | larval stage, with Scer\GAL4^ap-md544

Nop60B^GD16822

increased cell death | recessive

Nop60B¹

increased cell death | third instar larval stage, with Scer\GAL4^ap-md544

Nop60B^GD16822

increased cell death | third instar larval stage, with Scer\GAL4^bi.PU

increased cell death | third instar larval stage, with Scer\GAL4^en.PU

Nop60B^GD16822

increased cell number | third instar larval stage, with Scer\GAL4^bi.PU

increased cell number | third instar larval stage, with Scer\GAL4^en.PU

Nop60B^GD16822

increased occurrence of cell division | third instar larval stage, with Scer\GAL4^bi.PU

Nop60B^GD16822

increased occurrence of cell division | third instar larval stage, with Scer\GAL4^en.PU

Nop60B^GD16822

melanotic mass phenotype | larval stage, with Scer\GAL4^Act5C.PU

Nop60B^GD16822

some die during embryonic stage | recessive

some die during larval stage, with Scer\GAL4^Act5C.PU

Nop60B^GD16822

some die during larval stage, with Scer\GAL4^ap-md544

Nop60B^GD16822

some die during larval stage | recessive

some die during pupal stage, with Scer\GAL4^pnr-MD237

Nop60B^GD10940

some die during pupal stage | recessive

Nop60B^k06308

visible, with Scer\GAL4^Act5C.PI

Nop60B^RNAi.Sym.UAS

visible, with Scer\GAL4^Act5C.PU

Nop60B^GD16822

visible, with Scer\GAL4^bi.PU

Nop60B^GD16822

visible, with Scer\GAL4^Bx-MS1096

Nop60B^GD16822

visible, with Scer\GAL4^en.PU

Nop60B^GD16822

visible, with Scer\GAL4^nub-AC-62

Nop60B^GD16822

visible, with Scer\GAL4^pnr-MD237

visible, with Scer\GAL4^vg.int2.1

Nop60B^GD16822

visible | conditional | somatic clone

Nop60B^k05318

visible | recessive

Nop60B¹

Phenotype manifest in

Allele

adult abdomen & macrochaeta

Nop60B¹

adult cuticle & adult abdomen

Nop60B¹

adult cuticle & adult abdomen, with Scer\GAL4^Act5C.PI

Nop60B^RNAi.Sym.UAS

adult thorax, with Scer\GAL4^pnr-MD237

Nop60B^RNAi.sp.UAS

anterior-posterior compartment boundary of the wing disc | third instar larval stage, with Scer\GAL4^bi.PU

Nop60B^GD16822

chaeta, with Scer\GAL4^Act5C.PI

Nop60B^RNAi.Sym.UAS

chaeta, with Scer\GAL4^pnr-MD237

cytosolic large ribosomal subunit, with Scer\GAL4^nanos.PG

Nop60B^GL00555

cytosolic small ribosomal subunit, with Scer\GAL4^nanos.PG

Nop60B^GL00555

egg

Nop60B¹

egg chamber

Nop60B¹

egg chamber | absent, with Scer\GAL4^nanos.PG

embryo

Nop60B¹

female germline 8-cell cyst | increased number, with Scer\GAL4^nanos.PG

Nop60B^GL00555

ganglion mother cell | larval stage, with Scer\GAL4^insc-Mz1407

germarium, with Scer\GAL4^nanos.PG

Nop60B^GL00555

germline cell | adult stage | male

Nop60B^DL4

hub cell

Nop60B^DL4

larval neuroblast | larval stage, with Scer\GAL4^insc-Mz1407

male germline stem cell

Nop60B^DL4

mesonotum, with Scer\GAL4^pnr-MD237

nucleolus, with Scer\GAL4^nanos.PG

Nop60B^GL00555

nurse cell & nucleus

Nop60B¹

oocyte, with Scer\GAL4^nanos.PG

Nop60B^GL00555

spectrosome | decreased number, with Scer\GAL4^nanos.PG

Nop60B^GL00555

spermatocyte fusome

Nop60B^DL4

testis

trichogen cell, with Scer\GAL4^pnr-MD237

Nop60B^GD10940

wing, with Scer\GAL4^ap-md544

Nop60B^GD16822

wing, with Scer\GAL4^bi.PU

Nop60B^GD16822

wing, with Scer\GAL4^nub-AC-62

Nop60B^GD16822

wing | conditional | somatic clone

Nop60B^k05318

wing blade, with Scer\GAL4^vg.int2.1

Nop60B^GD16822

wing disc, with Scer\GAL4^ap-md544

Nop60B^GD16822

wing disc, with Scer\GAL4^en.PU

Nop60B^GD16822

wing disc | third instar larval stage, with Scer\GAL4^bi.PU

Nop60B^GL00555

wing disc posterior compartment | third instar larval stage, with Scer\GAL4^en.PU

Nop60B^GD16822

wing margin, with Scer\GAL4^Bx-MS1096

Nop60B^GD16822

wing margin, with Scer\GAL4^en.PU

Nop60B^GD16822

wing margin, with Scer\GAL4^vg.int2.1

Nop60B^GD16822

wing margin bristle, with Scer\GAL4^en.PU

Nop60B^GD16822

wing margin bristle, with Scer\GAL4^vg.int2.1

Nop60B^GD16822

wing pouch | third instar larval stage, with Scer\GAL4^bi.PU

Nop60B^GD16822

wing vein, with Scer\GAL4^en.PU

Nop60B^GD16822

wing vein, with Scer\GAL4^nub-AC-62

Nop60B^GD16822

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (3)

Hsap\DKC1

14 of 14

Yes

Hsap\TRUB1

3 of 14

Yes

Hsap\TRUB2

2 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (3)

Rnor\Dkc1

13 of 14

Yes

Rnor\Trub1

3 of 14

Yes

Rnor\Trub2

2 of 14

Mus musculus (laboratory mouse) (3)

Mmus\Dkc1

13 of 14

Yes

Mmus\Trub1

3 of 14

Yes

Mmus\Trub2

2 of 14

Xenopus tropicalis (Western clawed frog) (3)

Xtro\dkc1

7 of 13

Yes

Xtro\trub1

1 of 13

Xtro\trub2

1 of 13

Danio rerio (Zebrafish) (3)

Drer\dkc1

14 of 14

Yes

Drer\trub1

3 of 14

Yes

Drer\trub2

2 of 14

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\K01G5.5

14 of 14

Yes

Cele\Y43B11AR.3

2 of 14

Anopheles gambiae (African malaria mosquito) (2)

Agam\AgaP_AGAP004739

12 of 12

Yes

Agam\AgaP_AGAP002077

2 of 12

Arabidopsis thaliana (thale-cress) (2)

Atha\NAP57

13 of 13

Yes

Atha\AT5G14460

3 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\CBF5

13 of 13

Yes

Scer\PUS4

3 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\cbf5

12 of 12

Yes

Spom\SPBC11C11.10

3 of 12

Yes

Escherichia coli (enterobacterium) (1)

Ecol\truB

5 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Nop60B. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (1)

CG7849

2 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

dyskeratosis congenita, X-linked

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 6 )

Allele

Disease

Evidence

References

Nop60B^GL00555

model of dyskeratosis congenita

CEA

(Vicidomini et al., 2015)

Nop60B^DL10

model of X-linked dyskeratosis congenita

CEA

(Kauffman et al., 2003)

Nop60B^DL4

model of X-linked dyskeratosis congenita

CEA

(Kauffman et al., 2003)

Nop60B^DL6

model of X-linked dyskeratosis congenita

CEA

(Kauffman et al., 2003)

Nop60B^k05318

model of X-linked dyskeratosis congenita

CEA

(Tortoriello et al., 2010)

Nop60B^GD16822

model of dyskeratosis congenita

CEA

(Vicidomini et al., 2015)

model of X-linked dyskeratosis congenita

CEA

(Tortoriello et al., 2010)

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

DKC1; dyskerin pseudouridine synthase 1

model of X-linked dyskeratosis congenita

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)

Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

DKC1; dyskerin pseudouridine synthase 1

14 of 14

300126

X-linked dyskeratosis congenita

TRUB1; TruB pseudouridine synthase family member 1

3 of 14

610726

Functional Complementation Data

Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.

Interactions

Summary of Physical Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

Nop60B - Pi3K21B

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Nop60B - Ras85D

anti tag coimmunoprecipitation, peptide massfingerprinting

(Friedman et al., 2011)

Nop60B - S6kII

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Nop60B - foxo

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Nop60B - rictor

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Nop60B - vas

anti tag coimmunoprecipitation, western blot, Identification by mass spectrometry

(Durdevic and Ephrussi, 2019)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Nop60B

suppressible

raptor

(Breznak et al., 2023)

Nop60B

suppressible

(Vicidomini et al., 2015)

Nop60B

enhanceable

(Vicidomini et al., 2015)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Subunit Structure (UniProtKB)

Component of the box H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex consisting of Nop60B, Gar1, NPH2 and Nop10, and associated with H/ACA-type snoRNAs.

(UniProt, O44081 )

Linkouts

BioGRID - A database of protein and genetic interactions.

63449

DroID - A comprehensive database of gene and protein interactions.

FBgn0259937

MIST (genetic) - An integrated Molecular Interaction Database

37873

MIST (protein-protein) - An integrated Molecular Interaction Database

37873

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Ribosome biogenesis in eukaryotes

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Telomere Extension By Telomerase

Class of Gene

gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-106

Cytogenetic map

60C1-60C2

Sequence location

2R:24,174,877..24,186,343 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

60C1-60C2

Limits computationally determined from genome sequence between P{EP}EP503 and P{lacW}Nop60B^k05318

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

60B12-60C1

(Giordano, 1998.9.2)

60C1-60C2

(determined by in situ hybridisation)

(Spradling et al., 1999)

60B-60C

(determined by in situ hybridisation)

(Giordano et al., 1999)

60B13-60C1

(determined by in situ hybridisation)

(Phillips et al., 1998)

60C1-60C2

(Beaton, 1997.12.27)

60B12-60B13

60C1--2

(BDGP Project Members, 1994-1999)

Experimentally Determined Recombination Data

Location

2-106

(FlyBase, 2016)

2-110.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (14)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

36595

y¹ v¹; P{TRiP.GL00555}attP2

85620

w¹¹¹⁸; PBac{WH}Nop60B^f01318/CyO

65634

w¹¹¹⁸; PBac{IT.GAL4}Nop60B^1245-G4

44888

y¹ w^*; Mi{MIC}Nop60B^MI07849

12202

y¹ w^67c23; P{lacW}Nop60B^k05318/CyO

76957

y¹ sc^* v¹ sev²¹; P{TKO.GS00695}attP40

79436

y¹ sc^* v¹ sev²¹; P{TOE.GS01351}attP40

57500

y¹ sc^* v¹ sev²¹; P{TRiP.HMC04815}attP40

Kyoto

102462

y¹ w^67c23 ; P{lacW}Nop60B^k06308 / CyO

VDRC

v109616

P{KK101240}VIE-260B

v34597

w¹¹¹⁸; P{GD10940}v34597

v318245

PBac{fTRG00888.sfGFP-TVPTBF}VK00033

More stocks available...

Genomic Clones (25)

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (126)

Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

FBgn0259937

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0259937

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Riccardo et al., 2007, Phillips et al., 1998)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

dsRNA made from templates generated with primers directed against this gene results in a change in cell proliferation.

(Guertin et al., 2006)

One of 42 Drosophila genes identified as being most likely to reveal molecular and cellular mechanisms of nervous system development or plasticity relevant to human Mental Retardation disorders.

(Inlow and Restifo, 2004)

Nop60B hosts the snoRNA:H1 gene in its fourth intron. Overall orientation not stated: Nop60B+ snoRNA:H1 + Nop60B+

(Giordano et al., 1999)

Nop60B plays a central role in ribosomal RNA processing and pseudouridylation.

(Giordano et al., 1999)

The 3' exons of Nop60B are non-coding and correspond to Uhg6, a snoRNA host gene.

(FlyBase, 1996-)

Relationship to Other Genes

Source for database merge of

Source for merge of: l(2)k05318 Nop60B

(Phillips et al., 1998)

Source for merge of: Nop60B Uhg6

(FlyBase, 1996-)

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Nop60B CG3333

(Wang, 1999.11)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (17)

Reported As

Symbol Synonym

CG3333

(National Institute of Genetics Fly Stocks, 2022-, Kolkhof et al., 2017, Neuert et al., 2017, Çiçek et al., 2016, Hosono et al., 2015, Ding et al., 2014, Ni et al., 2011.7.19, Ni et al., 2010.12.1, Deloger et al., 2009, Keleman et al., 2009.8.5, Kroiss et al., 2009, Huang et al., 2005, Accardo et al., 2004)

DKC1

(Sanchez et al., 2016)

NOP60B

(Breznak et al., 2023, Dezi et al., 2016)

Nop60

(Grewal et al., 2007)

Nop60B

(Peng and Zhao, 2026, Duan et al., 2025, Stark et al., 2025, Gui et al., 2023, Känel et al., 2022, Pasquier and Robichon, 2022, Lindsey et al., 2021, Aboukilila et al., 2020, Baral et al., 2020, Sriskanthadevan-Pirahas et al., 2018, Neuert et al., 2017, Pritykin et al., 2017, Transgenic RNAi Project members, 2017-, Clandinin and Owens, 2016-, Sarov et al., 2016, Tan et al., 2016, Aradska et al., 2015, Herter et al., 2015, Kwong et al., 2015, Liang et al., 2014, Yasunaga et al., 2014, Jagut et al., 2013, Zoranovic et al., 2013, Friedman et al., 2011, Marinho et al., 2011, Neumüller et al., 2011, Tiwari et al., 2011, Kong et al., 2010, Rhodes et al., 2010, Demontis and Perrimon, 2009, Kroiss et al., 2009, Pierce et al., 2008, Teleman et al., 2008, Orian et al., 2007, Secombe et al., 2007, Guertin et al., 2006, Accardo et al., 2004, FlyBase, 1996-)

Nop60B/mfl

(Angrisani et al., 2015)

Nop60B/mnf

(Kučerová et al., 2016)

Nop60b

(Destefanis et al., 2020, Deloger et al., 2009, Riccardo et al., 2007)

Uhg6

(Pritykin et al., 2017)

dUhg6

(Huang et al., 2005)

l(2)k05318

mfl

(Song et al., 2023, Vicidomini et al., 2015, Tortoriello et al., 2010, Tortoriello et al., 2009, Riccardo et al., 2007, Accardo et al., 2004, Riccardo et al., 2003, Giordano et al., 2002, Giordano et al., 1999, Giordano, 1998.10.6)

minifly

(Jagut et al., 2013)

nop60B

(Jagut et al., 2013, Kauffman et al., 2003)

Name Synonyms

Minifly

(Kroiss et al., 2009)

Nucleolar protein at 60B

(FlyBase, 1996-)

Uhg6

dUhg-like 6

(Qu and Huang, 2004.11.1)

minifly

(Jagut et al., 2013, Tortoriello et al., 2010, Riccardo et al., 2007, Jorgensen and Tyers, 2004, Tycowski and Steitz, 2001, Giordano et al., 1999)

Secondary FlyBase IDs

FBgn0023184
FBgn0022178
FBgn0083122

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 71 )

Sequence Crossreferences

NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

37873

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

O44081

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

O44081

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

O44081

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

37873/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0259937

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0259937

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG3333

MARRVEL_MODEL - MARRVEL (model organism gene)

37873

Linkouts

BioGRID - A database of protein and genetic interactions.

63449

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0259937

DroID - A comprehensive database of gene and protein interactions.

FBgn0259937

DRSC - Results frm RNAi screens

FBgn0259937

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Nop60B_1

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0259937

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG3333

Flygut - An atlas of the Drosophila adult midgut

FBgn0259937

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0259937

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC010569

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Ribosome biogenesis in eukaryotes

MIST (genetic) - An integrated Molecular Interaction Database

37873

MIST (protein-protein) - An integrated Molecular Interaction Database

37873

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Telomere Extension By Telomerase

References (127)

The following external sites may use different assemblies or annotations than FlyBase.

-0.39

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