FlyBase Gene Report: Dmel\PH4αNE3

General Information

Symbol

Dmel\PH4αNE3

Species

D. melanogaster

Name

prolyl-4-hydroxylase-alpha NE3

Annotation Symbol

CG31017

Feature Type

protein_coding_gene

FlyBase ID

FBgn0051017

Gene Model Status

Current

Stock Availability

3 publicly available

Enzyme Name (EC)

procollagen-proline 4-dioxygenase (1.14.11.2)

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

100A1-100A1

Sequence location

3R:30,604,181..30,606,144 [+]

Recombination map

3-101

RefSeq locus

NT_033777 REGION:30604181..30606144

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 (4 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables iron ion binding

inferred from electronic annotation with InterPro:IPR006620

(InterPro Project Members, 2004-)

enables L-ascorbic acid binding

inferred from electronic annotation with InterPro:IPR006620

(InterPro Project Members, 2004-)

enables procollagen-proline 4-dioxygenase activity

inferred from biological aspect of ancestor with PANTHER:PTN004202971

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR013547

(InterPro Project Members, 2004-)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in endoplasmic reticulum

inferred from biological aspect of ancestor with PANTHER:PTN004202971

(GO Reference Genome Project, 2011-)

located_in endoplasmic reticulum

inferred from electronic annotation with InterPro:IPR013547

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

PEPTIDYL-PROLINE DIOXYGENASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

procollagen-proline 4-dioxygenase activity

2-oxoglutarate + L-prolyl-[collagen] + O2 = CO2 + succinate + trans-4- hydroxy-L-prolyl-[collagen] (1.14.11.2)

RHEA 18945:

Summaries

Gene Group (FlyBase)

PEPTIDYL-PROLINE DIOXYGENASES -: Peptidyl-proline dioxygenases catalyze the hydroxylation of peptidyl L-proline to peptidyl hydroxy-L-proline, where 2-oxoglutarate and one other act as hydrogen or electron donors with incorporation of one atom of oxygen into each donor.

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\PH4αNE3 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 Q961I8)

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 5.47

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

PH4αNE3-RA

FBtr0085667

NM_143557

1627

481

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

PH4αNE3-PA

FBpp0085029

55.9

481

5.29

Q961I8

NP_651814

AAN14251

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q961I8

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\PH4αNE3 using the Feature Mapper tool.

External Data

Crossreferences

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

PH4alphaNE3_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).

-0.06

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\PH4αNE3 in JBrowse

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

View exonic expression by developmental stage for Dmel\PH4αNE3

View exonic expression by tissue for Dmel\PH4αNE3

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

326114/tissue=All

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

FBgn0051017

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0051017

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

FBgn0051017

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

CG31017

Flygut - An atlas of the Drosophila adult midgut

FBgn0051017

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 2 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of PH4αNE3

Transgenic constructs containing regulatory region of PH4αNE3

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3R)Exel7378

(Ryder, 2004.4.26)

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

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

PH4αNE3^GD10133

viable, with Scer\GAL4^Mef2.PR

PH4αNE3^GD10133

viable, with Scer\GAL4^pnr-MD237

PH4αNE3^GD10133

Phenotype manifest in

Allele

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) (4)

Hsap\P4HA1

6 of 14

Yes

Hsap\P4HA3

6 of 14

Yes

Hsap\P4HA2

5 of 14

Hsap\P4HTM

4 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) (4)

Rnor\P4ha1

6 of 14

Yes

Rnor\P4ha2

6 of 14

Yes

Rnor\P4ha3

6 of 14

Yes

Rnor\P4htm

3 of 14

Yes

Mus musculus (laboratory mouse) (4)

Mmus\P4ha1

6 of 14

Yes

Mmus\P4ha2

6 of 14

Yes

Mmus\P4ha3

5 of 14

Mmus\P4htm

4 of 14

Yes

Xenopus tropicalis (Western clawed frog) (7)

Xtro\p4ha1

4 of 13

Yes

Xtro\p4ha2

3 of 13

Xtro\p4ha3

2 of 13

Xtro\p4htm

2 of 13

Yes

Xtro\LOC100492280

1 of 13

Xtro\lztr1

1 of 13

Xtro\st18

1 of 13

Danio rerio (Zebrafish) (9)

Drer\p4ha1a

7 of 14

Yes

6 of 14

6 of 14

6 of 14

5 of 14

4 of 14

Yes

Drer\p4htmb

4 of 14

Yes

Drer\LOC110438249

1 of 14

Yes

Drer\LOC110438585

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (6)

Cele\dpy-18

6 of 14

Yes

Cele\phy-2

6 of 14

Yes

Cele\C14E2.4

3 of 14

Yes

Cele\phy-3

3 of 14

Yes

Cele\Y43F8B.19

3 of 14

Yes

Cele\phy-4

2 of 14

Yes

Anopheles gambiae (African malaria mosquito) (3)

Agam\AgaP_AGAP000971

6 of 12

Yes

Agam\AgaP_AGAP004611

5 of 12

Agam\AgaP_AGAP013377

4 of 12

Arabidopsis thaliana (thale-cress) (13)

Atha\AT-P4H-1

9 of 13

Yes

Atha\AT1G20270

8 of 13

Yes

Atha\AT3G28480

8 of 13

Yes

Atha\AT3G28490

8 of 13

Yes

Atha\AT4G33910

8 of 13

Yes

Atha\AT4G35810

8 of 13

Yes

Atha\AT4G35820

8 of 13

Yes

Atha\AT5G18900

8 of 13

Yes

Atha\AT5G66060

8 of 13

Yes

Atha\P4H2

8 of 13

Yes

Atha\P4H5

8 of 13

Yes

Atha\P4H13

8 of 13

Yes

Atha\AT4G25600

4 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:PH4αNE3. 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) (25)

12 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

10 of 13

10 of 13

10 of 13

10 of 13

10 of 13

10 of 13

10 of 13

9 of 13

9 of 13

9 of 13

7 of 13

6 of 13

6 of 13

5 of 13

5 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 ( 0 )

Human Ortholog

Disease

Evidence

References

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?

P4HA1; prolyl 4-hydroxylase subunit alpha 1

6 of 14

176710

P4HA3; prolyl 4-hydroxylase subunit alpha 3

6 of 14

608987

P4HA2; prolyl 4-hydroxylase subunit alpha 2

5 of 14

600608

MYOPIA 25, AUTOSOMAL DOMINANT; MYP25

P4HTM; prolyl 4-hydroxylase, transmembrane

4 of 14

614584

HYPOTONIA, HYPOVENTILATION, IMPAIRED INTELLECTUAL DEVELOPMENT, DYSAUTONOMIA, EPILEPSY, AND EYE ABNORMALITIES; HIDEA

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.

FBgn0051017

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

procollagen hydroxylation and glycosylation

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

External Data

Linkouts

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

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-101

Cytogenetic map

100A1-100A1

Sequence location

3R:30,604,181..30,606,144 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

100A1-100A1

Limits computationally determined from genome sequence between P{PZ}ncd⁰⁵⁸⁸⁴ and P{lacW}l(3)s2500^s2500

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-101

(FlyBase, 2016)

3-98.5

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (3)

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

Bloomington

65351

y¹ sc^* v¹ sev²¹; P{TRiP.HMC06103}attP40

VDRC

v21281

w¹¹¹⁸; P{GD10133}v21281

v21284

w¹¹¹⁸; P{GD10133}v21284

Genomic Clones (14)

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

cDNA Clones (1)

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

GH21465

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.

FBgn0051017

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0051017

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Relationship to Other Genes

Source for database merge of

Additional comments

Source for identity of PH4αNE3 CG9708 was sequence comparison ( date:020425 ).

(FlyBase Genome Annotators, 2002-2003, FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: PH4αNE3 CG9708

(Abrams, 2002.3.26, FlyBase, 1996-)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (4)

Reported As

Symbol Synonym

CG31017

(Perkins et al., 2009)

CG9708

(Abrams, 2002.3.26)

PH4αNE3

Name Synonyms

prolyl-4-hydroxylase-alpha NE3

(Abrams and Andrew, 2002)

Secondary FlyBase IDs

FBgn0039791

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 38 )

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.

326114

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.

Q961I8

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

Q961I8

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.

Q961I8

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

326114/tissue=All

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

FBgn0051017

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

FBgn0051017

FlyMine - An integrated database for Drosophila genomics

FBgn0051017

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

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

dme:Dmel_CG31017

MARRVEL_MODEL - MARRVEL (model organism gene)

326114

Linkouts

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

FBgn0051017

DroID - A comprehensive database of gene and protein interactions.

FBgn0051017

DRSC - Results frm RNAi screens

FBgn0051017

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

PH4alphaNE3_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0051017

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0051017

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

procollagen hydroxylation and glycosylation

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

CG31017

Flygut - An atlas of the Drosophila adult midgut

FBgn0051017

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

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

References (26)

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

-0.06

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