FlyBase Gene Report: Dmel\NHP2

General Information

Symbol

Dmel\NHP2

Species

D. melanogaster

Name

NHP2

Annotation Symbol

CG5258

Feature Type

protein_coding_gene

FlyBase ID

FBgn0029148

Gene Model Status

Current

Stock Availability

8 publicly available

Gene Summary

Component of the box H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA (Probable). 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 (By similarity). H/ACA snoRNP complex-dependent ribosome biogenesis is important in female germline cell differentiation during oogenesis (PubMed:37343092). (UniProt, Q9V3U2)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

70F6-70F6

Sequence location

3L:14,801,328..14,802,168 [-]

Recombination map

3-42

RefSeq locus

NT_037436 REGION:14801328..14802168

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 (8 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 box H/ACA snoRNA binding

inferred from biological aspect of ancestor with PANTHER:PTN000560394

(GO Reference Genome Project, 2011-)

enables RNA binding

inferred from electronic annotation with InterPro:IPR050257

(InterPro Project Members, 2004-)

Biological Process (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in germarium-derived cystoblast division

inferred from mutant phenotype

(Morita et al., 2018)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in rRNA pseudouridine synthesis

inferred from sequence or structural similarity with UniProtKB:P32495

(Gene Ontology Curators, 2002-)

inferred from biological aspect of ancestor with PANTHER:PTN000560394

(GO Reference Genome Project, 2011-)

involved_in snRNA pseudouridine synthesis

inferred from biological aspect of ancestor with PANTHER:PTN000560394

(GO Reference Genome Project, 2011-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in nucleolus

inferred from direct assay

(Morita et al., 2018)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

part_of box H/ACA snoRNP complex

inferred from biological aspect of ancestor with PANTHER:PTN000560394

(GO Reference Genome Project, 2011-)

traceable author statement

(Breznak et al., 2023)

part_of sno(s)RNA-containing ribonucleoprotein complex

inferred from sequence or structural similarity with UniProtKB:P32495

(Gene Ontology Curators, 2002-)

Gene Group (FlyBase)

H/ACA SMALL NUCLEOLAR RIBONUCLEOPROTEIN COMPLEX

Protein Family (UniProt)

Belongs to the eukaryotic ribosomal protein eL8 family. (Q9V3U2)

Protein Signatures (InterPro)

Summaries

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).

Protein Function (UniProtKB)

(UniProt, Q9V3U2)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\NHP2 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 Q9V3U2)

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

Gene model reviewed during 5.46

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

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

NHP2-RA

FBtr0075698

NM_143708

667

160

NHP2-RB

FBtr0333076

NM_001274920

781

160

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

NHP2-PA

FBpp0075448

17.7

160

8.30

FBpp0305289

17.7

160

8.30

Q9V3U2

NP_001261849

AGB94542

Polypeptides with Identical Sequences

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

160 aa isoforms: NHP2-PA, NHP2-PB

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

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, Q9V3U2)

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\NHP2 using the Feature Mapper tool.

External Data

Crossreferences

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

NHP2_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).

-0.18

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism | ubiquitous

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

anterior endoderm

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

inclusive hindgut primordium

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in nucleolus

inferred from direct assay

(Morita et al., 2018)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\NHP2 in JBrowse

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

View exonic expression by developmental stage for Dmel\NHP2

View exonic expression by tissue for Dmel\NHP2

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

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0029148

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

44005/tissue=All

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

FBgn0029148

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0029148

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

FBgn0029148

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

CG5258

Flygut - An atlas of the Drosophila adult midgut

FBgn0029148

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\NHP2

Stages(s) 4-6
Stages(s) 7-8
Stages(s) 9-10
Stages(s) 11-12
Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 1 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 9 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of NHP2

Transgenic constructs containing regulatory region of NHP2

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 2 )

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

NHP2^GD13496

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

NHP2^GD13496

viable, with Scer\GAL4^pnr-MD237

NHP2^GD13496

viable, with Scer\GAL4^tin.CΔ4

NHP2^GD13496

Sterility

Allele

female sterile, with Scer\GAL4^nanos.PG

Other Phenotypes

Allele

abnormal cell number | adult stage, with Scer\GAL4^{VP16.nanos.UTR}

increased cell death | adult stage, with Scer\GAL4^{VP16.nanos.UTR}

NHP2^HMC03339

visible, with Scer\GAL4^pnr-MD237

NHP2^GD13496

Phenotype manifest in

Allele

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

embryonic/larval fat body | third instar larval stage, with Scer\GAL4^{SPARC-MI00329-GAL4}

NHP2^GL01315

extracellular matrix | third instar larval stage, with Scer\GAL4^{SPARC-MI00329-GAL4}

NHP2^GL01315

female germline cyst, with Scer\GAL4^{VP16.nanos.UTR}

germarium, with Scer\GAL4^nanos.PG

NHP2^HMC03339

germarium, with Scer\GAL4^{VP16.nanos.UTR}

NHP2^HMC03339

trichogen cell, with Scer\GAL4^pnr-MD237

NHP2^GD13496

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) (8)

Hsap\NHP2

14 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

Yes

Hsap\RPS12

1 of 14

Hsap\RSL1D1

1 of 14

Hsap\RSRC1

1 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) (11)

Rnor\Nhp2

12 of 14

Yes

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Rnor\Rps12

1 of 14

Rnor\Rsl1d1l1

1 of 14

Mus musculus (laboratory mouse) (8)

Mmus\Nhp2

13 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

Yes

Mmus\Rsl1d1

1 of 14

Mmus\Rsrc1

1 of 14

Xenopus tropicalis (Western clawed frog) (3)

Xtro\nhp2

11 of 13

Yes

Xtro\s100z

1 of 13

Yes

Xtro\snu13

1 of 13

Danio rerio (Zebrafish) (8)

Drer\nhp2

14 of 14

Yes

Drer\rpp38

2 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (4)

Cele\Y48A6B.3

14 of 14

Yes

Cele\rps-12

2 of 14

Cele\snu-13

2 of 14

Cele\rpl-7A

1 of 14

Anopheles gambiae (African malaria mosquito) (5)

Agam\AgaP_AGAP012204

12 of 12

Yes

2 of 12

2 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (9)

Atha\AT5G08180

13 of 13

Yes

Atha\AT2G47610

2 of 13

Atha\AT3G62870

2 of 13

Atha\AT4G01790

2 of 13

Yes

2 of 13

2 of 13

2 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (5)

Scer\NHP2

13 of 13

Yes

2 of 13

2 of 13

2 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (5)

Spom\nhp2

12 of 12

Yes

2 of 12

2 of 12

1 of 12

1 of 12

Escherichia coli (enterobacterium) (1)

Ecol\rplA

1 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:NHP2. 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) (7)

4 of 13

3 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

NHP2; NHP2 ribonucleoprotein

model of autosomal recessive dyskeratosis congenita 2

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?

NHP2; NHP2 ribonucleoprotein

14 of 14

606470

DYSKERATOSIS CONGENITA, AUTOSOMAL RECESSIVE 2; DKCB2

autosomal recessive dyskeratosis congenita 2

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

RNA-protein

Physical Interaction

Assay

References

NHP2 - Sxl

clip, quantitative reverse transcription pcr

(Morita et al., 2018)

protein-protein

Physical Interaction

Assay

References

NHP2 - CG3224

experimental knowledge based

(Guruharsha et al., 2011)

NHP2 - rictor

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

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

NHP2

enhanceable

Sxl

(Morita et al., 2018)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Sxl

suppressible

NHP2

(Morita et al., 2018)

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, Q9V3U2 )

Linkouts

BioGRID - A database of protein and genetic interactions.

68768

DroID - A comprehensive database of gene and protein interactions.

FBgn0029148

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

44005

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

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-42

Cytogenetic map

70F6-70F6

Sequence location

3L:14,801,328..14,802,168 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

70F6-70F6

Limits computationally determined from genome sequence between P{PZ}Mpcp⁰⁰⁵⁶⁴ and P{PZ}l(3)rO220^rO220

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

70F-70F

(Renault, 1999.12.17)

Experimentally Determined Recombination Data

Location

3-42

(FlyBase, 2016)

3-36.3

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (8)

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

Bloomington

51784

y¹ v¹; P{TRiP.HMC03339}attP40

79661

y¹ sc^* v¹ sev²¹; P{TOE.GS01221}attP40

83447

y¹ sc^* v¹ sev²¹; P{TKO.GS03495}attP40

42479

y¹ sc^* v¹ sev²¹; P{TRiP.GL01315}attP2/TM3, Sb¹

NIG-Fly

5258R-1

P{NIG.5258R}1

HMC03339

y¹ v¹; P{TRiP.HMC03339}attP40

VDRC

v35729

w¹¹¹⁸; P{GD13496}v35729

v35730

w¹¹¹⁸; P{GD13496}v35730

Genomic Clones (14)

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

cDNA Clones (58)

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

RH66170

Other clones

DPiM_RH66170

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.

FBgn0029148

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0029148

Antibody Information

Laboratory Generated Antibodies

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 in combination with dsRNA against gig results in suppression of the final average cell size, with it being closer to the control average cell size, rather than the average cell size resulting from knockdown of the candidate gene alone.

(Guertin et al., 2006)

Relationship to Other Genes

Source for database merge of

Source for merge of: NHP2 CG5258

(Bayraktaroglu, 2000.8.7)

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (3)

Reported As

Name Synonyms

NHP2

Secondary FlyBase IDs

FBgn0036452

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 37 )

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.

44005

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.

Q9V3U2

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

Q9V3U2

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

M9PCI2

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.

Q9V3U2

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0029148

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

44005/tissue=All

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

FBgn0029148

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

FBgn0029148

FlyMine - An integrated database for Drosophila genomics

FBgn0029148

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

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

dme:Dmel_CG5258

MARRVEL_MODEL - MARRVEL (model organism gene)

44005

Linkouts

BioGRID - A database of protein and genetic interactions.

68768

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

FBgn0029148

DroID - A comprehensive database of gene and protein interactions.

FBgn0029148

DRSC - Results frm RNAi screens

FBgn0029148

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

NHP2_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0029148

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0029148

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

CG5258

Flygut - An atlas of the Drosophila adult midgut

FBgn0029148

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

TC012019

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

Ribosome biogenesis in eukaryotes

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

44005

References (55)

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

-0.18

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