FlyBase Gene Report: Dmel\rnh1

General Information

Symbol

Dmel\rnh1

Species

D. melanogaster

Name

ribonuclease H1

Annotation Symbol

CG8729

Feature Type

protein_coding_gene

FlyBase ID

FBgn0023171

Gene Model Status

Current

Stock Availability

5 publicly available

Enzyme Name (EC)

ribonuclease H (3.1.26.4)

Gene Summary

ribonuclease H1 (rnh1) encodes a RNA-DNA hybrid ribonuclease. [Date last reviewed: 2019-09-12] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

RNase H1, l(2)k07624, l(2)43F1-5

Key Links

Genomic Location

Cytogenetic map

43F2-43F2

Sequence location

2R:7,931,054..7,932,380 [-]

Recombination map

2-57

RefSeq locus

NT_033778 REGION:7931054..7932380

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 (7 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables RNA-DNA hybrid ribonuclease activity

inferred from direct assay

(Filippov et al., 1997)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables magnesium ion binding

inferred from electronic annotation with InterPro:IPR017067

(InterPro Project Members, 2004-)

enables nucleic acid binding

inferred from electronic annotation with InterPro:IPR002156, InterPro:IPR036397

(InterPro Project Members, 2004-)

enables RNA-DNA hybrid ribonuclease activity

inferred from biological aspect of ancestor with PANTHER:PTN000068227

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR002156, InterPro:IPR017067

(InterPro Project Members, 2004-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in mitochondrial DNA replication

inferred from mutant phenotype

(González de Cózar et al., 2019)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in DNA replication, removal of RNA primer

inferred from biological aspect of ancestor with PANTHER:PTN000068227

(GO Reference Genome Project, 2011-)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

located_in mitochondrion

inferred from direct assay

(González de Cózar et al., 2019)

located_in nucleus

inferred from direct assay

(González de Cózar et al., 2019)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

RNA-DNA HYBRID RIBONUCLEASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

RNA-DNA hybrid ribonuclease activity

Endonucleolytic cleavage to 5'-phosphomonoester (3.1.26.4)

Summaries

Gene Snapshot

ribonuclease H1 (rnh1) encodes a RNA-DNA hybrid ribonuclease. [Date last reviewed: 2019-09-12]

Gene Group (FlyBase)

RNA-DNA HYBRID RIBONUCLEASES -: RNA-DNA hybrid ribonucleases are endonucleases that catalyze the hydrolysis of the RNA strand in an RNA-DNA hybrid to generate 5_ phosphate and 3_ hydroxyl ends. (Adapted from PMID:18261820).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\rnh1 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 Q7JY33)

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

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

Gene model reviewed during 5.49

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

rnh1-RA

FBtr0088883

NM_057967

1108

333

rnh1-RB

FBtr0088884

NM_206055

1051

314

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

rnh1-PA

FBpp0087959

37.1

333

8.93

FBpp0089188

35.2

314

9.23

A1Z768

NP_995777

AAS64899

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

333 (aa); 37 (kD predicted)

(Filippov et al., 1997)

Comments

External Data

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\rnh1 using the Feature Mapper tool.

External Data

Crossreferences

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

rnh1_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).

2.59

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in mitochondrion

inferred from direct assay

(González de Cózar et al., 2019)

located_in nucleus

inferred from direct assay

(González de Cózar et al., 2019)

Expression Deduced from Reporters

Reporter: P{lacW}rnh1^k07624

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 11 -- 17

central nervous system

(Filippov et al., 2001)

larval ventral nerve cord

(Filippov et al., 2001)

larval stage

brain | faint

(Filippov et al., 2001)

gonad

(Filippov et al., 2001)

embryonic/larval proventriculus | distal

(Filippov et al., 2001)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\rnh1 in JBrowse

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

View exonic expression by developmental stage for Dmel\rnh1

View exonic expression by tissue for Dmel\rnh1

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

35746/tissue=All

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

FBgn0023171

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0023171

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

FBgn0023171

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

CG8729

Flygut - An atlas of the Drosophila adult midgut

FBgn0023171

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 6 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 8 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of rnh1

Transgenic constructs containing regulatory region of rnh1

Aberrations (Deficiencies and Duplications) ( 6 )

Inferred from experimentation ( 6 )

Gene disrupted in

Df(2R)BSC265

(Christensen and Cook, 2007.3.22)

Df(2R)CA53

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

Df(2R)Exel6055

(Ryder, 2004.4.26)

Df(2R)nap16

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

Gene not disrupted in

Df(2R)H3C1

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

Df(2R)ST1

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

Inferred from location ( 0 )

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 | recessive

lethal - all die before end of prepupal stage | recessive

lethal - all die before end of pupal stage

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

rnh1^GD5333

viable, with Scer\GAL4^Mef2.PR

rnh1^GD5333

viable, with Scer\GAL4^pnr-MD237

rnh1^GD5333

viable, with Scer\GAL4^tin.CΔ4

rnh1^GD5333

Other Phenotypes

Allele

abnormal developmental rate

rnh1¹

melanotic mass phenotype | prepupal stage | recessive

rnh1¹

some die during prepupal stage | recessive

some die during pupal stage

Phenotype manifest in

Allele

embryonic/larval central nervous system

rnh1¹

imaginal disc | larval stage

rnh1¹

melanotic mass

rnh1¹

prepupa | prepupal stage P4(ii)

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) (1)

Hsap\RNASEH1

14 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (1)

Rnor\Rnaseh1

14 of 14

Yes

Mus musculus (laboratory mouse) (1)

Mmus\Rnaseh1

13 of 14

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\rnaseh1

11 of 13

Yes

Xtro\LOC100493932

1 of 13

Yes

Xtro\ttc38

1 of 13

Yes

Danio rerio (Zebrafish) (1)

Drer\rnaseh1

14 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (7)

Cele\rnh-1.0

13 of 14

Yes

Cele\rnh-1.3

6 of 14

Yes

Cele\K12D12.5

4 of 14

Yes

Cele\rnh-1.2

4 of 14

Yes

Cele\rnh-1.1

3 of 14

Yes

Cele\T09F3.5

3 of 14

Yes

Cele\T09F3.4

2 of 14

Yes

Anopheles gambiae (African malaria mosquito) (1)

Agam\AgaP_AGAP008088

12 of 12

Yes

Arabidopsis thaliana (thale-cress) (3)

Atha\AT1G24090

2 of 13

Yes

Atha\AT3G01410

2 of 13

Yes

Atha\AT5G51080

2 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\RNH1

12 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\rnh1

11 of 12

Yes

Escherichia coli (enterobacterium) (1)

Ecol\rnhA

8 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:rnh1. 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) (0)

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

RNASEH1; ribonuclease H1

model of autosomal recessive progressive external ophthalmoplegia with mitochondrial DNA deletions 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?

RNASEH1; ribonuclease H1

14 of 14

604123

PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE 2; PEOB2

autosomal recessive progressive external ophthalmoplegia with mitochondrial DNA deletions 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

esyN Network Diagram

Interactions Browser

MIST Molecular Interaction Search Tool

Summary of Genetic Interactions

esyN Network Diagram

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0023171

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

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

DNA replication

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-57

Cytogenetic map

43F2-43F2

Sequence location

2R:7,931,054..7,932,380 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

43F2-43F2

Limits computationally determined from genome sequence between P{lacW}lin19^k01207&P{lacW}rnh1^k07624 and P{lacW}CSN4^k08018&P{lacW}l(2)k08504^k08504

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

43F1-43F2

(determined by in situ hybridisation)

(Spradling et al., 1999)

43F-43F

(determined by in situ hybridisation)

(Filippov et al., 1997)

43F1-43F5

(determined by in situ hybridisation)

(Filippov et al., 1997)

43F1-43F2

43F3--4

(BDGP Project Members, 1994-1999)

Experimentally Determined Recombination Data

Location

2-57

(FlyBase, 2016)

2-57.2

(Comeron et al., 2012)

(Filippov et al., 1997)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

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

Bloomington

10677

y¹ w^67c23; P{lacW}rnh1^k07624/CyO

Kyoto

111220

y^d2 w¹¹¹⁸ P{ey-FLP.N}2 P{5xglBS-lacZ.38-1}TPN1; P{neoFRT}42D P{lacW}rnh1^k07624 /CyO y⁺

NIG-Fly

2RG-1433

y² VhaAC39-1^cho-1 v¹; P{U6-rnh1.NIG.sgRNA}attP40/CyO

VDRC

v109457

P{KK109098}VIE-260B

v15533

w¹¹¹⁸; P{GD5333}v15533

Genomic Clones (9)

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

cDNA Clones (42)

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

AT19436

Other clones

DPiM_AT19436

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.

FBgn0023171

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0023171

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

New stable cell line derived from S2-unspecified : S2 cells expressing Tag:HA -tagged mtSSB and Tag:V5 -taggeds rnh1 were created.
(González de Cózar et al., 2020)

Other Comments

The l(2)43F1-5 mutants contain P-element insertion in the open reading frame of rnh1.

(Filippova et al., 1998)

Gene isolated in a screen of the second chromosome identifying mutants affecting disc morphology.

(Roch et al., 1998)

rnh1 is required for imaginal disc morphogenesis.

(Filippov et al., 1997)

rnh1 has been cloned.

(Filippov et al., 1997)

Relationship to Other Genes

Source for database merge of

Source for merge of: rnh1 l(2)43Fa

(Filippova et al., 1998)

Source for merge of: rnh1 l(2)k07624 l(2)k07409

(Spradling et al., 1999)

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (12)

Reported As

Symbol Synonym

74/9

(Roch et al., 1998)

CG8729

(National Institute of Genetics Fly Stocks, 2022-, Çiçek et al., 2016, Fukuoh et al., 2014, Keleman et al., 2009.8.5)

RNase H1

(Munden et al., 2022, González de Cózar et al., 2020, Filippov et al., 2001)

RnH1

l(2)43F1-5

(Filippov et al., 1997)

l(2)43Fa

l(2)k07409

l(2)k07624

(BDGP Project Members, 1994-1999)

rnh1

(González de Cózar et al., 2019, Kim and Choe, 2014, Japanese National Institute of Genetics, 2012.5.21, Christensen and Cook, 2007.3.22)

rnhl

(Elmore and Smith, 2001)

Name Synonyms

RNaseH1

ribonuclease H1

(Spradling et al., 1999)

Secondary FlyBase IDs

FBgn0020291
FBgn0022077
FBgn0024594

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 44 )

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.

35746

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.

Q7JY33

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.

Q7JY33

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

35746/tissue=All

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

FBgn0023171

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

FBgn0023171

FlyMine - An integrated database for Drosophila genomics

FBgn0023171

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

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

dme:Dmel_CG8729

MARRVEL_MODEL - MARRVEL (model organism gene)

35746

Linkouts

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

FBgn0023171

DroID - A comprehensive database of gene and protein interactions.

FBgn0023171

DRSC - Results frm RNAi screens

FBgn0023171

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

rnh1_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0023171

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0023171

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

CG8729

Flygut - An atlas of the Drosophila adult midgut

FBgn0023171

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

TC004604

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

DNA replication

References (42)

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

2.59

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